Regenerators from RE4 should definitely be on this list. Not only do they take tons of damage and regrow their limbs, but after you've blown off their legs and feel like laughing at them for not being able to move, they slither MUCH faster than they were walking and jump at your neck. They also have a low, ragged breathing noise that if you don't hear early on they'll jump you. Jesus Christ I hate them.
Regenerators from RE4 are way scarier than Dr Salvador. When you first see them you can't even kill them. I remember the first time i was trapped in a narrow hallway in that lab, and as soon as i heard that breathing i knew that i was probably going to die, or flee from my TV first.
Pyramid Head(s) is my #1 favorite video game villain. He not only rapes monsters, he ripped off a girl's skin and raped the remains in the movie! BTW Check out YGOTAS-37, Bakura vs. Bonz & Pyramid Head vs. Nemesis. FYI Pyramid Head humps Nemesis.
Shodan and Pyramids have got to be the scariest dudes. I don't own either game, but when I watched their clips, it scared the shit out of me (luckily not literately). I wish something liek that would go in to a KH game. They get too boring because there's nothing you can't beat. It's never scary, except for Seph, but that's about it.