
User Interface
Often ignored, so it'll get first mention here. mdcertainty rules in this area. I've had ideas for what could be done to the interface, but never done them. mdcertainty has actually put the effort in and made some great little improvements, though.
Icons: Chaos, Dark Eldar, Eldar, Necrons, Sisters of Battle and Space Marines, plus Hero icons, mdcertainty replaced the original icons with better quality in-game shots
HUD: Dark Eldar and Imperial Guard, mdcertainty made some well-themed changes to both interfaces
Badges and banners
The undisputed champions have to be Hangar-8 and Joril. Hangar-8 showed what great quality we could get out of a comparatively small image, and the community followed.
In the best of the rest, I've always been quite pleased with the detail I managed in my Crimson Fists, Mentor Legion and Dark Angels packs. Ariesatyre's Complete Tau set eclipses my attempts at a full set of Tau badges. Finally, Sgt.Roadkill did a useful job with his Generic Guard badges to increase the choice for Guard Commanders.
Utilities
Where would we be without the useful utilities? Even though he gave instructions on making your own, Hangar-8's wrinkle sheet must have been used by loads of banner makers since it was released.
In other areas, Hangar-8's simple Shoulder upgrade removal tool was a saving grace to remove the horrible "glowing skulls of doom" that appeared on Space Marine shoulders after the Bionics upgrade, making them look completely ridiculous.
This section also inevitably has a good bit of self-promotion, so I'll keep it short: Dawn of War Texture Tool for modifying any texture, and the various different UberPainter versions for checking the textures in the Army Painter. The SGA Explorer and IChunky Viewer could also have been very useful, but never seem to have found their niche.
Textures and patterns
This is going to be a big list, so I'll leave it until later!