So the question is simple: which of these do you use in an active game?
Also, an elaboration on the nature of your use is welcome. While this year's poll is far more complex than previous ones, I don't think I can account for each combination available.
For those who may not be entirely familiar with the acronyms, here is the explanation:
http://planetelderscrolls.gamespy.com/View.php?view=utilities.detail&id=8 -- Morrowind Enhanced
The earliest of the third party applications, made by Aerelorn. It is utilized by mods such as Combat Enhanced, Blocking Enhanced, Writing Enhanced, Oblivion-Style Spellcasting, and more. The link here goes to the dev kit, which actually includes v1.6, the latest version of the program. It is considered by many to be inherently unstable; however many of the mods it makes possible cannot be duplicated with other utilities.
http://sourceforge.net/projects/mwse/ -- Morrowind Script Extender
An external program that adds extra script functions to the game of Morrowind. This allows for the creation of plugins that are impossible or at least very difficult while running the game alone. At this point there are several dozen mods made for it, offering a wide variety of new features and game behavior.
http://sourceforge.net/projects/morrgraphext/ -- Morrowind Graphics Extender
MGE is a project that wraps the various DirectX dlls used by Morrowind. Despite it's name, it wraps the input and sound dlls as well as graphics. It also interfaces with MWSE to make even more functions available to modders. It enables features such as distant land, bloom, hdr, and many more.
http://www.fliggerty.com/phpBB3/viewtopic.php?f=53&t=1008 -- Morrowind Code Patch
This is considered by many to be the indispensable bug fix utility. It actually patches the exe file to address many bugs in the engine, as well as add/modify some features. All changes made are optional. It does not run in the background, but rather is something that you only need to run once.