Aliens vs Predator: Extinction desperately needs a sequel, one of the best AvP games out there.
Some good choices so far, I'd love to see a sequel for Valkyria Chronicles or Mirror's Edge.
But to add something of my own: Vampire: The Masquerade - Bloodlines. Think Deus Ex with vampires. I was never into vampires and no, it's not because of the whole Twilight fad, I just never got into the idea of them period. However, VtMB had me loving them. You could pick amongst many different kinds of vampires which all have their own abilities. You have to blend in with society while still having your powers and using them in missions. It's still the closest game I have seen to being Deus Ex without actually being Deus Ex. I'm open to suggestions if you have something you think is closer though. :D
Mirror's Edge; Freedom Fighters; Republic Commando; Deus Ex: Human Revolution (with Jensen back); Turok; I really thought that game was fine, but improved on where needed in a sequel would make it a fantastic experience, while the first was merely 'really good', and almost great. The Bourne Conspiracy; I think anyone that hasn't played it should give it a chance, and anyone that may have just breezed through it and may have no thought much of it need to try it again like I did, on its hardest difficulty; great game. I'd love to see another Chronicles of Riddick game from Starbreeze 'cause while I liked Dark Athena, I wouldn't consider that to be a sequel. I think--while I don't necessarily care for it too much now--there needs to be an Advent Rising sequel, and finally, I think there needs to be a TimeSplitters sequel. Actually, I have one more, I'd love to see a sequel to Brothers in Arms with Matt Baker. There are probably more, but that's all I have in mind. I'll come back if I think I have more.
Edit: Oh yeah, and I think Dante's Inferno needs one as well. I liked that game, though it had... problems.
Shenmue 2 - Let's just get this over with already, it's taken long enough. Whatever, it'll probably never happen.
Dead Rising 2 - Dead Rising is still one of my favorite new IPs this generation and i would love to see Frank return in a proper sequel instead of being a model swap.
Onimusha - We need more Onimusha, but more like the firs two and a lot less like Dawn of Dreams.