Tropic Thunder is about a group of actors making a war movie in Southeast Asia. Supposedly, there's a character in the film who's trying to transition from action movies to more serious fare, and so there are several discussions about playing mentally handicapped characters. Though I haven't seen the movie yet, it's totally obvious to me that it's not making fun of the mentally handicapped, but rather Hollywood clichés regarding movies about the mental handicapped, and the actors that play them.
Also, the advocacy groups shouldn't be upset, because chances are the retards in the audience won't be offended since they can't understand anything happening on-screen anyway. In fact, it occurs to me that if a retarded person was to get offended by Tropic Thunder, it might mean that he was faking.
P.S. If you're part of an advocacy group, and you didn't understand what I just did, then feel free to protest me. I could use the publicity.
UPDATE: My review of Tropic Thunder