Dawnguard, Heartfire, and one of the other main ones I believe.
Yeah, just never EVER, clean Skyrim.ESM. Bad things will happen. you should clean Dawnguard, Hearthfire, and Update.
I would recommend watching Gopher's video http://www.youtube.com/watch?v=UOQO2S6HDBw&list=UU1CSCMwaDubQ4rcYCpX40Eg&index=5&feature=plcp and reading the Cleaning Guide.
http://skyrim.nexusmods.com/mods/25859
http://www.creationkit.com/index.php?title=TES5Edit_Cleaning_Guide_-_TES5Edit