It's a tie between Psychonauts, American McGee's Alice (creepiest damn game EVER), and the co-op for Psi-Ops. It involved one person controlling movement and the other controlling firing weapons, switching weapons, and using powers. It was actually pretty cool.
Oh, and Pac-Txt, cool at first, but it gets boring after eating about two dots.
And if you're gonna go into Hentai Games, X-play did a special on them once. There was one titled "Do You Like Horny Bunnies" and for some reason was about librarians. Also, tentacle rape. Lots and lots of tentacle rape.