Tes3Mod:Repairing Saves

Morrowind save files can become corrupted in a number of ways:
Bad references
Orphan contents
Debris records
Doubling
Bad references for global scripts

Wrye Mash
Repair All
Fortunately, many (but definitely not all) of these problems can be fixed with a single menu command on Wrye Mash. Simply go to the saves tab, right click on the problem save file and select Repair All.
Doing this will fix bad references, orphan contents and debris records.
However, it will not fix doubling that has already occurred and it will not fix doubling that is already locked into the savegame.

Remove Bethesda Doors
Wrye Mash does have the ability to remove a specified set of references from the game. Since doors are particularly prone to doubling, removing door references will have the effect of removing all door doubles. However, it will also reset any other doors. I.e., if you lock-picked the door, you'll now find it locked again.
If there are other objects which are repeatedly doubled in your files, then you may be able to create additional ref removers for them. However, note that ref removers will also reset/remove any legitimate copies of those items, so be careful!

Mod Specific Cleaning
Note that if you use Mash to remove a mod from a savegame's master list, you automatically remove all of the references placed by that mod. 
Follow this up with a "Repair All" to remove any debris records (globals, npcs, etc.) associated with the removed mod.
If you leave the mod unselected (and removed from your load list), then Morrowind will complete the removal process.

Enchanted Editor
 Nuclear Option
An older method of cleaning save games is to simply delete cell records from the savegame. While using Wrye Mash's Repair All is generally a better solution, there may be some cases when the EE Nuke is desirable. (The solution is particularly nuclear when you remove all but a few cell records.)
Advantages
All doubles and other problem references are removed.
Savegame can be substantially reduced in size, resulting in improved performance.
Disadvantages
Quests may break, companions may reset, etc.

Manual Repair
Enchanted editor gives you pretty complete control over the records and subrecords in the Morrowind savegame. If you know what you're doing, you can delete specific subrecords and edit other records to remove problems.
E.g., you could use EE to fix the reference pointer for a global script. 
Considerations
The understanding of the TES3 file format has continued to improve over time. As a result the ESTemplate.ini file that comes with EE is out of date. Note that the Wrye Mash distribution comes with a fairly recent ESTemplate.ini file in its extras folder.
While EE understands mod files very well, it's understanding of save games is not so good. In particular, it doesn't correctly recognize how spawned creatures are embedded in spawn points, how references are moved out of cells, and how persistent references are separated from non-persistent references. Hence if you use the safe edit option, you may run into problems in some cases. 
Always make a backup or duplicate of your savegame before working on it in EE, and then test play your changes afterwards to see if they look correct.
If you know what you're doing, you may want to turn off safe editing in EE.

In Game Manual Cleaning
You can manually remove doubles while in game using the console.
Process
Open the console, and click on the suspected double.
Type ori into the console. This will list the origin of the reference. If the file name is "None" then that's the double. If the file name is not "None" then click on the other instance of the object and try ori on it.
Note that getting a "File: None" does not prove that the object is a double, since this happens naturally for many objects in the game (e.g., for all items that you drop while in game). The ori trick is only useful when you're looking at two (or more) copies of an object and you know that only one of them is the correct one.
To delete the double.
Type "disable" into the console and hit return.
Type "setdelete 1" into the console and hit return.
Note that if you disable but don't delete, then the references is still there, albeit invisible. It's better to disable the double and delete, rather than just disable.