The game I just really really really want a sequel to is Rune. I hope that after Humanhead is done playing around with Prey 2 that they start working on a sequel which they multiple times said they wanted to make, sadly I doubt it's ever going to be successful. It's just... the things they could do on a modern engine, again it's old school arena brawling gameplay won't probably appeal to todays audience.
Runner up: mothereffin' Dungeon Keeper. Seriously EA don't just waste this IP on a Korean MMO.
Honourable mentions:
Evil Genius (I'll take this over not having a Dungeon Keeper 3)
Vampire: The Masquerade - Bloodlines
Beyond Good and Evil
Star Wars: Republic Commando (instead of games it got continued in comic form)
Star Wars: Battlefront
Psychonauts
Brütal Legend
Kingdom Hearts 2 (Seriously Square, stop with the spin-offs, just give us the real deal already)
Mercenaries (How about a sequel to that game that DOESN'T suck.)
There's probably tons more that I can't think of at the moment.