Garrador From Resident Evil 4
I know the Resident Evil series is well known for having bosses that are freaky as fuck, and picking just one was very difficult. Though Nemesis was relentlessly scary, and even El Gigante would beat out Gassador for many people, I just felt there was a realness to Garrador that you did not commonly find in Resident Evil games.
He was just a blind dude kept in a dungeon, who goes ape shit when he hears sounds and tries to kill people with his man-made and Wolverine-esque claws. While I am not so scared of some giant beast who can uproot trees and swing them like baseball bats, there is a part of me that knows there is probably a Garrador locked in some basement somewhere, just waiting for some sound to lunge at.
Plus, you have to fight his ass in that little cage the second time, which makes it even more daunting (and there are two, so apparently someone mass produces these fucking freaks). That chainsaw wielding motherfucker with the burlap sack over his head is pretty damn scary, too, but he is never technically a boss. And although Garador is only a mini-boss, he is creepy as hell, so it felt like a perfect note to the end the list on.
Now quick, someone comment about how I should have had that giant, singing pile of shit from the Conker games on this list. Someone NEEDS to comment that, stat!