In my opinion, "cult classic" means it sold badly, possibly got good reviews, but disappeared off the radar and didn't get nearly as much praise it deserved In short, "Deus Ex" and "Bioshock" can't qualify because they were successful; same with anything that got a sequel. With that said, my picks:
-"Psychonauts." No duh on that one
-"Vampire the Masquerade: Bloodlines." Based off an iffy pen-and-paper RPG with its own cult following, buggy and released too soon by a harsh publisher, forcing the great developer (Troika) to go under... but still a solid, smart, dark and fun game.
-"Uru: Ages Beyond Myst." A fantastic adventure game, one of the first with a real and detailed 3D world(s) that wasn't focused on finding objects to rub against other objects. Devious puzzle logic, too... one of the worlds was literally designed to be a giant puzzle system leading to a king's treasure vault. UbiSoft abandoned the online world portion, which is a shame... I was in the beta, and I can tell you it was the most intelligent online community I've ever been in.
-"Beyond Good and Evil." Cheesy animal characters and voice acting aside, the game was solid, polished, and had a dark and complex story. Probably also the first game to really incorporate photography into gameplay until "Dead Rising" came along.
-"XIII." This one's a bit iffy, but I think it should be included. A decent FPS, the first to try cell-shaded comic book aesthetics, and a rather complex and interesting storyline involving political intrigue, assassination, conspiracy and mistaken identity. Not to mention Adam West and David Duchovney providing voice work. :-D