Until 1999, anyway.
Heh, that’s totally true about Affleck and Damon, especially when they work with Kevin Smith. And James Cromwell supposedly played a kindly farmer in Babe, but I’ll never get past his performance as Dudley Smith in L.A. Confidential. Chilling.
Whenever I see Jake Busey, I always expect a psycho, maybe a deranged redneck/hillbilly psycho, perhaps a Bible verse-spouting psycho.
“Hey, It’s That Guy!” character actor Billy Drago always plays knife-wielding toadies, flunkies, and psychos, as in The Untouchables and Adventures of Brisco County, Jr…
Danny Trejo will always be “evil badass Mexican,” whether he’s a thug, a hitman, a prisoner, or a vampire (or perhaps all of the above).
Admittedly, his character in Garden State wasn’t the world’s most upstanding citizen, but he turned out to be a good guy in that one.
Any celebrity guest star in any Law and Order show will probably turn out to be the perp.
In Blast from the Past Christopher Walken was not a bad guy, nor did I get the feeling that he would turn out evil.
Gary Oldman - he’s playing the Devil, Dracula, Lee Harvey Oswald, a crazed cop, Pontius Pilate, an evil Senator, Dr Smith, a serial killer, a religious fanatic, and Sid Vicous. Makes me wonder if Beethoven was secretly killing co-eds.
Well, the crazy Russian on the space station wasn’t a bad guy, was he? But not a good guy, either. Oh, heck. I don’t remember. (Aah. Armageddon. Grade D movie with a Grade A cast.)
Tracey Walter isn’t an automatic bad guy. But as soon as you see him, you know that his character is going to pass along a crucial piece of information.
Christian Bale, because of American Psycho and The Machinist, and Edward Norton, because of… well… pretty much everything.
“I’m gonna need a handsaw.”
–Jack Bauer, season 2 of 24
I dunno, Smoochy was a pretty upstanding rhino.
I’m not sure about Sarsgaard, either. I can only recall seeing him in Jarhead, where he’s among the more responsible and level-headed characters for most of the movie.
“If that’s John Saxon, I’m screwed.”
Just about the worst case of someone turning out to be the bad guy was Kim Cattrall’s role in Star Trek VI: The Undiscovered Country. Somebody aboard the Enterprise is a traitor, but the only Enterprise crew members who’ve had speaking parts are Kirk, Spock, McCoy, Chekov, Scott, Uhura and… Lieutenant Valeris.
Well, let’s see, by process of elimination the guilty party is… wait, let me guess… Ensign Ricky!
HACKsaw. 
You know when Al Pacino played the good guy in “Heat” I just could NOT for the life of me, get my brain to compute.
Serious? I kept expecting the end to go like this:
JD: Hey, Peter, why’d you bring us down into this spooky deserted quarry?
Peter Saarsgard: This isnt a quarry…this is YOUR GRAVE!!
(Pushes JD and Natalie into the quarry, cackling like fuck.
Plus a somewhat camp and crazy, but definitely evil, Satan in Constantine.
So are you saying it was him that unleashed the evil worm beasties on that unsuspecting hamlet in Tremors? And perhaps it was really him that killed Sean Penn’s daughter in Mystic River? Gosh, who knew? 
Oh, please. Stop slandering Boromir.
No, Sean Bean is Richard Sharpe! I always have a difficult time believing he’s the bad guy.
Richard Kiel, if not the evil Eegah, then a wicked henchman.
Vincent Price, for sure. Although, it’s weird to see LAURA which is early in his career, before he got type-cast… and he’s not the villain, although I kept expecting him to be!