Jacob and Ashely from Mass Effect. They are both pretty deep, likeable, and (in Ashely's case) believably flawed characters who unfortunately get completely overlooked because they aren't fan bait or alien.
Tidus from Final Fantasy X. The guy is a brilliant take on the idea of noble self-sacrifice, and it's also refreshing to see a JRPG protagonist who, for the most part, is a pretty open and cheerful guy. He doesn't play up trying to be a stoic or badass, nor do they try to make him "cool". But for some reason, many FF fans just don't seem to like him. Inherent bias against a "jock" character, perhaps?
Doctor Strange. The guy has got connections to nearly every major hero organization in the Marvel-verse, and power coming out the wazoo, but he very rarely actually DOES anything. I know non-interference is part of the deal and being the Sorcerer Supreme is something of a full-time job, but really, the guy is basically unknown in the public consciousness precisely because he's never given the chance to shine.
Reaver from Fable 2 and 3. Get's a lot of hate for killing likable characters and generally being an asshat to the PC and those around him. But really, how do you think the PC comes across to everyone else when you are being evil? It's actually pretty clever, and nice to see the idea that "Not all Heroes are heroic" put into practice outside of your own actions.
Sofia Lamb from Bioshock 2. She was a MUCH more effective villain than either Ryan or Fontaine.
