Ok, we'll go more recent, all of these are 2009 or later:
-Crysis 2
-Alien Breed: Impact
-Alpha Protocol
-The Ball
-Mass Effect 2
-Metro 2033
-Sid Meier's Civilization V
-The Misadventures of P.B. Winterbottom
-Batman: Arkham Asylum
-DiRT 2
-Mirror's Edge
-Osmos
[..]
My Documents. The new default location for any documents that the user creates. Applications should be written to save files here by default.
[..]
I may be pressing this a bit, but just trying to demonstrate that the documents folder is also a standard, and the app data folder is very difficult for a new windows user to find. To prove my point, I asked two friends and my parents if they could find their "app data" folder. They could not. They didn't think to type it in or enable hidden folders, like your average windows user. I just think it would be best to be more user friendly. Some of these games that use the appdata folder, such as Modern Warfare 2, rarely, if ever, need you to ever interact with the files that are saved there, which are pretty much limited to game saves and other data they would have no use for. On the other hand, Glest (MegaGlest) would need very accessible data because mods are installed to this folder, as well as the INI, since these things can't be done in-game.
Notice how modable games tend to use the documents folder, eg: Civilization)?
Also, I seem to have forgotten the most important game on this list which uses the user folder: Glest Advanced Engine. It is very easy to find, without even needing to ask, contrast to the MegaGlest folder, where someone would almost always have to look it up unless they have experience with the appdata folder (again: most windows users do not). I hope when the merger occurs, you will go with that folder.