Halo 3.
I hate Halo 3 for having a hideously short campaign mode. What was that, 6 hours? Maybe? What a letdown. The only thing I can think of that annoyed me more was Fable, and it's 8 hour storyline. It's a fucking RPG for christ's sake. /facepalm
Despite the short campaign, Halo 3 was still the best game in the series. It was really a great game, and fully utilized the engine that the Xbox 360 supplied it.
System Shock...I've heard about it, and looked it up and whatnot. I can't really play it though, it was for DOS and Macintosh. (On a side-note, I really miss being able to access DOS on Windows. Oh well.) No matter, it can't trump Halo 3.