This is going to sound geeky and lame, but... Star Trek: Deep Space Nine. This series has been going south since around the start of the fifth season, though. Characters acting in contradiction to what they're supposed to be like, and the show embracing religion, even though ST has always seemed pretty much opposed to it.
Oh, and Perception.
I think that sort of thing is what put me off DS9. Plus, it's the only Star Trek that I don't have on DVD (Although, I've always liked Odo :happy.