Many different ones, I hope I get them all together:
7zip and WinRar for extracting mods and creating mod packages
BSA Unpacker for extracting the BSAs
BSA Registration Utility
Der Fix-Wie-Nix-übersetzer for translating Mods into German
Enchanted Editor for manually editing esps
http://timeslip.users.sourceforge.net/exeopt.html to improve game stability
http://www.ntcore.com/4gb_patch.php - ditto
http://planetelderscrolls.gamespy.com/View.php?view=Utilities.Detail&id=84 - saves multiple quichsaves
FPS Optimizer v1.96 - mainly for scaling the interface
MGE XE - the latest beta
MWSE - included in MGE XE
Morrowind Code Patch 2.1
NifSkope - for quick uv fixes and retextures (and some more things)
http://www.nexusmods.com/skyrim/mods/12801/? - for, well, optimizing textures
TESTool - to merge objects
TES3cmd - to clean mods and merge leveled lists
https://github.com/Yacoby/Wrye-Mash/downloads - for changing load order, repairing saves, updating master lists, installing and uninstalling mods and more
AstroGrep and TextCrawler - to search within files (e.g. to find out which nif files use a certain texture or which mod changes a specific thing)
http://www.nexusmods.com/morrowind/mods/475/? - to identify mod conflicts
Sketchup with many different plugins - for creating new meshes
Blender with http://niftools.sourceforge.net/ - for editing meshes
Photoshop and Gimp - for creating textures
http://www.crazybump.com/ - for creating Normal maps (https://sites.google.com/site/ccdsurgeon/home after trial expired)
Construction set
Microsoft Editor - mainly for creating readme files
Wow, that was a lot. I hope I got everything.