Kratos from the God of war series. As much fun as it is to play the character, I really can not be friends with a person who has such a low opinion on the value of life. I mean sure other characters kill but Kratos has made me wince in sympathy for Greek monsters. That really should not be possible.
Also, Raziel from the Legacy of Kain series. I understand his motivation but he really comes off as a self righteous prick sometimes. Oddly enough, Kains' dedication to honesty (no matter how horrible he acts otherwise) earns him just enough respect in my eyes to keep our interactions civil. If I weren?t food to him of course.
Ambassador Udina from Mass Effect. I viewed him as just another politician at first, nothing to get worked up over. By the end of the game I wanted to sock him in the mouth, then kick him when he is down. The council got more sympathy from me, and those guys almost had me tearing my hair out at points.
The entire caste from the Sonic The Hedgehog series. Sonic, Tails, and Knuckles were charming, once. Now I would honestly like to see all of them, heroes and villains, killed, dipped in honey glaze, roasted over an open flame, and then fed to the hogs.
Finally, every sentient thing in Warhammer 40K. The entire crapsack universe needs to collapse in one itself, and a new and less horrible universe born to take its place. Also, I would pay good money to watch Galactus eat holy terra and the "God-Emperor" of mankind with it.