If I had to pick just one, it'd be Cowboy Bebop. I liked it until I realized it had 40 minutes of plot in a 26 episode series. It was the first series I ever saw that I felt it would have worked better as a movie.
Other series/movies people love that I hate include Ninja Scroll, Ghost in the Shell, Akira, Full Metal Panic, Kenshin, Haibane Renmei, Love Hina, Hellsing, School Days (except for Kotonoha. I love her), and everything from Studio Ghibli or directed by Miyazaki. Oh, and I also didn't think much of the Haruhi anime, but the novels are far superior. There's tons more I could add to the list, but I suppose I'll leave that for another thread.