This is a collection of notes, compiled by me, the main source of information was my experiences and the ES forum, specifically this thread and this thread. Credits go to everyone who contributed. If I took a post in almost its entirety, credits are given in italics below the section that they have written.

Index
Programs to change Load order
How to use the programs
General Rules
What mods need their load order changing?
How Morrowind handles plugins
How do you know what plugin has altered what
General Load Order
Ideas on what order to load your mods
Example Conflicts
TESTools Merged Objects

Programs to change Load order

TES Construction Set - Included with the game
The TES Construction Set is one of the worst ways of changing load order. It is very slow and cumbersome, the only up side is that it comes with the game, so you don't have to install any other programs/download anything.

Mlox - Google Code
Mlox is an automated tool that runs under Windows and Linux that attempts to set your load order based on a ruleset. It also proiveds warnings and information about conflicts. Very useful to use.

TESTool - Download TES Pluggins Tool 1.3
TESTool doesn't require any other programs to make it run, which is a large bonus. It is however only slightly better at reording mods than the TES Construction Set, as you can only move mods to the bottom.

It does however have many other useful features, including "Merge Objects"

Wrye Mash - Wrye Musings
This is in my opinion, the best tool for changing load order in the middle of a game, when you could cause doubling when using other methods. It is reasonably fast at mass reordering. It also requires Python

Reorder Plugins - Planet Elder Scrolls
The base of my ReOrder Mods program, it is a step forward from the TES CS and TESTool, but is a sep back in other ways. This enables you to Reorder mods with a move up and down button, but if you want to move something from the top of the list to the bottom, it becomes extremely tedious. It requires Java

Reorder Mods - Yacoby's Morrowind
I wrote this program, so I am biased, but I think this is the best program for reordering mods before starting a new game, unlike Wrye Mash, it is easier to use, can move several mods at once, and import and export load orders. The downside is it doesn't include any of the doubling prevention that Wrye Mash does. It also requires Microsoft .NET Framework

ReOrder Mods ++ - Yacoby's Morrowind
This is basically the same as ReOrder mods, so anything that apply's for that also apply's for this. The main difference is that ReOrder Mods ++ lacks some features, but doesn't require the .NET Framework

TES Plugin Conflict Detector - TESPCD
Without a doubt, this is a must have, as it allows you to (You'll never guess) check conflicts.What is great about it in this case is that it will give the conflict and base esp, and then the overriding one (aka, lower down in the load order), so you can see how your current load order is conflicting.

Programs Conclusion
ReOrder Mods or ReOrder Mods ++ are good for setting up a new set of mods, but Wrye Mash is amazing at changing load order while you have an active save game. It could be worth looking at the next section and deciding what you like best based on the screenshots. The TES Plugin Conflict Detector is another must have. TESTool is useful for Merging Objects
You should also check your load order with mlox as it is basicly a repository of knowlege about various plugins.

How to use the programs

Note: This section only contains information on how to reoreder mods with the specific program, it doesn't contain any information about how to install the said program. Please refer to the readme as to how to install

TES Construction Set
The first way is to open and save a mod, this only moves a mod to the end of the load order. This method is very slow to do, and can introduce GMSTs if done incorrectly

There is an way using the Construction Set - and that is to open it up. Then highlight each mod you want to move (click once, not twice) and put something in the 'description of mod' area - even a space will do. This will update the time and the header on the mod. Note: This won't visibly change the load order until you close and reopen the load window

1. Press to open the list of mods
2. Select the mod you want to alter
3. Change this in any way (I just add a space) to move the mod to the bottom of the load list (Note: You have to open and close the Data Files box to see changes)

The basic problem with each of these methods is that they simply move the mod to the end of the list and you still will have a lot of playing around to do. It can also cause doubling if load order is changed while using a saved game
[Lady Rae, ES Forum, Minor changes made]

TESTool

1. Press manage active plugins
2. Then press execute
3. Select the mods you want to reorder
4. This will reload the list
5. Press to move the selected mods to the bottom of the load list
6. OK to finish

Wrye Mash

1. This is what you change to change the last modified date
2. Hit save when you have to apply the changes
3. This is very useful, every time you start Mash, if any times are different from what they were, it will reset them to what they should be.

To alpeticaly order mods, select every mod (CTRL + A), then right click and File: Sort. They'll be placed at one minute intervals starting from the time/date of the current earliest mod.

The last version 0.65 of Wrye Mash also allows you to move a group of mods to a time/date that you specify. Within the group, the current ordering is kept, however, they're "compacted" so that they're within one minute intervals of each other. Again, select the mods you want to reorder, then right click and select "File: Redate...".

Reorder Plugins

1. Select the mod you want to move
2. Press up or down to move up or down
3. Press OK to apply changes

Reorder Mods

1. Select the mods you want to move
2. Move up, down, to the top or bottom
3. When you are done, press Reorder, and it will save the changes

ReOrder Mods ++
The method is exactly the same as the method for ReOrder Mods

TES Plugin Conflict Detector

Load the TES PCD, and press the Open button (1), select all your mods (Press Shift/Ctrl and click)

Then press the red arrow (2), and wait for it to load all the information

1. The ID of the conflict
2. Conflict type
3. The name of the conflicting entry
4. The overwriting file
5. The file that is being overwritten
6. The original file (The first file that contained that data)

See below for a tutorial like thing...

General Rules

There are no rules
That's right, there are no rules. There is no "load quest mods first" rule. No "load leveled lists last rule" it is all dependent on your mod list. Having said that, there is one rule:

Read the Readme!
This cannot be stressed enough, if you don't you are asking for trouble. The mods Readme will usually state if there are any major "Must be loaded after mod X" issues.

What mods need their load order changing?

Most mods don't need to be arranged, they can just be left where ever they land up.Thinks like face & hair mods (Not including Vampire face and hair), race mods, small clothing/armor/weapon mods that don't make any changes to existing NPC's, and quest mods that are set away from Vvardenfell & Solstheim.

Load order is important if the mod does any of the following:

1. Alter GMST's.
2. Makes changes to existing NPC's, creatures, or items.
3. Makes changes to the landscape around existing towns or structures.
4. Patch/Change another mod in some way
5. Vampire Mods

[Nerra, ES Forum, Minor Chages Made]

How Morrowind handles plugins

The way the Morrowind plugin system works is that the last loaded mod overwrites everything that it changes in every other mod before it. What is loaded first, and last is controlled by the last modified data of the file, so if mod1 had a last modified date of 05/06/2000, and Mod2 had a last modified date of 08/12/2005 Mod1 will be loaded first, and then Mod2, so if they both change the same thing, Mod2 will overwrite Mod1

So if we have two mods that both change a sword

(Loaded Mod1 first, then Mod2)

Mod1.esp
- weight = 150
- price = 200
- damage = 1-8
- 3d model = sword.nif

Mod2.esp
- weight = 120
- price = 250
- damage = 1-5
- 3d model = sword.nif

In the game, the Sword will have Mods2s stats as that was loaded last, overwriting mod1s stats
But if we change the load order so Mod2 is loaded first, and then Mod1

Mod2.esp
- weight = 120
- price = 250
- damage = 1-5
- 3d model = sword.nif

Mod1.esp
- weight = 150
- price = 200
- damage = 1-8
- 3d model = sword.nif

The sword will have Mod1s Stats, as that was loaded last.

There are ways to combine that stats of objects - See TESTools Merged Objects

How do you know what plugin has altered what?

So, you have your mod list of 100+ mods, but you need to know what alters what.
This is where the TES Plugin Conflict Detector (TESPCD) comes in. When you have chosen the mods that you are going to use and installed them, load up the TESPCD and do a full check

 

1. Press to open the options
2. Make sure this is checked
3. and these are checked

1. Open the files
2. Perform the check

You open multiple files using CTRL and click and/or Shift and click.

This should give you a big table full (or not so full) or conflicts

1. The ID of the conflict
2. Conflict type
3. The name of the conflicting entry
4. The overriding file
5. The file that is being overwritten
6. The original file (The first file that contained that data)

So you can see where there are conflicts. The "overriding file" is the file loaded later than the "Esp file", so the overriding file will take precedent. To change what file overwrites what, swap the order of the two mods around. It is worth noting that not all conflicts are bad, as they can be patches ect.

Also make sure to look at some Example Conflicts

General Load Order

As you may have already worked out, the ones at the bottom of the load list take precedent, they "win" so to speak. So really the more important the mod is to you, the lower down the list you load it.

For instance, you might put 'White Wolf of LoKKen' at the bottom of the list because you want to make sure the quests work perfectly or you might only want to walk around the landscape so you're probably going to want to put 'White Wolf of LoKKen' at the top of your list.
[Pseron Wyrd, ES Forum, Minor Changes Made]

Landscape
Back to the basics here. Morrowind is divided up into cells, so when ever the "Loading Area" comes up, you are moving from one cell to another.

In a esp or esm file, there is height data for each cell.

So when Mod1 make a mountain that covers two cells, and Mod2 makes a hole that covers one of the two cells, it is fairly obvious that we are going to get conflicts.

If we load Mod1 first, and then Mod2, when you visit the mountain, one of the cells will the mountain, and one of the cells will be the hole, and when the cells changes, there is a gap into nothingness.

Path grids
Path grids are the grids that tell the NPC's where to walk, without them there would be even more people falling into the river in Balmora ;)
Path grids are very similar to landscape, in that there can only be one for a cell, so you can see the problem. If Mod1 makes a house, and alters the path grid to go around the house, and then Mod2 alters the path grid in another part of town, but leaves the area when Mod1s house is the same as Morrowind.esm. When you load Mod1 and then Mod2, you are going to have NPC's trying to walk through a house, which they won't manage to do.

Landscape and Path grid Conclusion
When you start adding large mods, you are going to get conflicts like this (Landscape conflicts are more common and noticeable). Some of the older and less well made mods change landscapes when they don't need to, so if you make sure you load these mods earlier than the major landscape mods, you should be OK.

At some point, you will load two mods that have large landscape problems (Houses being buried, huge gaps in the land etc). The first thing I would do when this happens is look for patches, if I cannot find any I usually load up both the mods in the TESCS and have a look at them (If you have no experience with the TESCS, you may find it easier to at it in Morrowind, open the console and type TCL so that you can walk through objects).

I then try and change the order around, then taking another look, if it doesn't look to bad, I just stick with the current order.

If none of the above work, you have several options:

1. Don't use the two mods together
2. Fix the conflicts in the TESCS

Unfortunately the latter can take some time, and you do need some experience with the TESCS

Vampire Mods
Vampire mods deserve a special mention because there load order has to be totaly correct, or they will not work. See this list for a detailed order to put them in.

Changing Mod load order mid game
Changing mods in a running game is dangours, as you could get doubling:
Let's say you have 100 mods installed, now add #101. If you add it at position #50, all mods formerly #50, #51, ..., #100 will now become #51, #52, ..., #101. This causes problems.
[ps33, ES Forum, No Changes]

There are three ways to avoid this

1. Don't change mods while still using the same save
2. Only add mods the the end of your load list
3. Use Wrye Mash to add and remove mods

For anyone interested, Wrye explains why doubling occurs in much greater detail at Wrye Musings

Leveled lists
The game adds increasingly valuable items and increasingly tough creatures and NPCs to the world in response to player levels. It does this through leveled lists, which keep track of the player's level, gradually increasing the quality of items and toughness of enemies. The reason why you will never see a Golden Saint when you start a brand-new game is because the leveled lists prevent it.

When two mods alter the same leveled list the one nearer the bottom will over-ride the one above it. We get around this by extracting the lists and merging the changes into one .esp which goes at the bottom of your mod list, over-riding everything. TESTool and Wrye Mash can both merge leveled lists
[Pseron Wyrd, ES Forum, Minor changes made]

You do not need to load the leveled lists esp last, although you need to load it after any other mod that alters leveled lists. (So it is likely to be near the end).

Texture Packs
As most texture packs don't come with esps, you have to use install order to dictate what overwrites what. Simple, the ones that are installed later, overwrite the ones that were installed earlier.

Ideas on what order to load your mods

Idea #1
One school of though is that you load the simple little mods first, like mods that make the signs readable, and mods that give all the potions recognizable icons, etc. because they don't have really anything all that important and crucial which can cause conflicts. Conversely, large quest mods and game setting mods, and mods that do things like let you ride dragons, horses, boats, etc. can contain all manner of complicated scripts which can get a bit tricky, especially when save games can get dirtied by adding and removing mods without using Wrye Mash while still trying to use the same save.
[Qarl, ES Forum, Minor changes made]

Idea #2
Another idea is to put mods that change the heads/hair etc usually at the top. Let the middle take care of itself - unless you run into something mentioned in a readme, it is a very good idea to follow those.Then put 'tweaks' at the bottom - things like female versions of armor, clothes - that type of thing. And last is the file that use to change appearance of the NPCs around morrowind.
[Lady Rae, ES Forum, Changes made]

Conclusion
There is nothing saying you cannot combine theses ideas or/and throw in some of your own into the mix, as I have stated before, there are no rules...

Example Conflicts

This looks as though it should be conflicting. If you look at the mods (1), they both relate to vampires. Also, when we have a closer look at the conflicts (Double click), we see that the only thing that is different is the dialog, everything else (2) is the same. So it looks like it could be an intentional conflict. At this point you should read the readmes to check what order they should be loading in. (In this case we have the correct order)

This is a conflict between Deadric Sorcery and Were-Betterer(1). looking at the extended screens, you see that both mods add a script to the NPC(2). In the Were-betterer readme it says that it changes some no vital NPCs to be werewolves, so you can take a reasonable guess that this might be the case. Don't know what the OrcFavor script is, it could be very minor, or it could be extreamly major. So there are two ways you could go about it. You could either check out what the script does in the TESCS (This would require knowledge about scripting and the TESCS), or you could just guess.

With this order it comes down to which mod you want to work/have its full range of features... Totally up to you..

TESTools Merged Objects

About merging object:

Object are "definition" of an item that will be placed in game.
In the definition, you have several data like, for example:
- name of the corresponding mesh file (= name of the 3D model used by this object)
- kind of object: misc item, armor, weapon
- weight of the object
- price
- specific data: for armor -> armor rating, for weapon -> damage data
-...

(Morrowind loads last the most recent mods, so suppose for the following example that mod1 is the eldest, then there is mod2, and the most recent mod is mod3. Morrowind loads mod1, then mod2, and then mod3)

Object present in Morrowind.esm: example -> a sword:
- weight = 100
- price = 200
- damage = 1-5 pts (for each type of attack)
- 3d model = sword.nif

This sword is modified by mod1 with these data:
- weight = 150
- price = 200
- damage = 1-5
- 3d model = sword.nif

It is also modified by mod2:
- weight = 120
- price = 250
- damage = 1-5
- 3d model = sword.nif

And by mod3:
- weight = 100
- price = 200
- damage = 2-8
- 3d model = sword.nif

If you load only one of those 3 mods, well you'll obviously only get the modification of the weapon corresponding to the mod that you've chosen. If you load those 3 mods without changing or adding anything, the only data used by Morrowind are the data of the latest mod which is mod 3.

If you use the same mods, but you use the merge objects function, TES Tool is going to "scan" Morrowind and the mods. If one part of the definition of an object is modified, it'll add it to the new "merged objects" mod. If 2 mods are modifying the same part of the definition of an object, TES Tool use the last available data, which means that it takes the data that are from the latest mod.

In this example, TES Tool is going to scan Morrowind.esm:
- weight = 100
- price = 200
- damage = 1-5 pts
- 3d model = sword.nif

then it scans mod1, and you'll get a weapon like this:
- weight = 150
- price = 200
- damage = 1-5
- 3d model = sword.nif

Then it scans mod2 and the sword data are:
- weight = 120
- price = 250
- damage = 1-5
- 3d model = sword.nif

Then it scans mod3, and you'll get the final data (which will be stored in the merged_objects mod):
- weight = 120 (from mod2)
- price = 250 (from mod2)
- damage = 2-8 (from mod3)
- 3d model = sword.nif (from Morrowind, because none of the 3 mods is modifying this part of the definition of the sword)

The weight and the price data taken by TES Tool are from mod2 and not (as I wrote above) from the latest mod which is mod3. It is absolutely normal! It happens because weight and price data of mod 3 are exactly the same as the data of Morrowind.esm, which means that they're the same data of the game without any mods, and TES Tool doesn't care about data which are exactly the same as those initially present in the game. In any others cases, TES tool choose the latest data.

A summary of the paragraph above could be:
TES Tool choose the latest and modified data.

Now, if you change the date of modification of the 3 mods to get this order: mod2 (eldest), mod1, mod3(keep being the most recent), and you try to merge data of the sword, you'll get:
after scanning mod2:
- weight = 120
- price = 250
- damage = 1-5
- 3d model = sword.nif
after scanning mod1:
- weight = 150
- price = 250
- damage = 1-5
- 3d model = sword.nif
finally, after scanning mod3:
- weight = 150 (from mod1)
- price = 250 (from mod2)
- damage = 2-8 (from mod3)
- 3d model = sword.nif

And you see that you don't get the same merged_objects mod and that while playing in game, depending on the load order, you'll get a sword which won't be exactly the same. In this example, after changing load order, in the way I show it, the only thing that is changing is the weight of the sword, but any of the definition data of an object can be affected, depending on the mods you're using and on their load order.
[Bjam, ES Forum, Minor changes made]