I haven't seen anything too fancy for keeping track of module usage. If the OS keeps track of it in the file system you might be able to scoop off a last accessed date and roll your own.
Where I am working basically we all go through one person for module instalation. Otherwise you have to play with the modules in your own user space. It keeps things pretty clean, and if something breaks you know who to go bug :)
Personally though I don't see what the big deal of removing modules would be, and it may be a little dangerous to just go remove them even if they hadn't been used in a few months. Who's to say that somebody didn't bury a use command in an if statement and it just hadn't been called yet.
I guess I don't see the harm in keeping a few extra megs worth of unused modules around myself.
