Parker, from the “Richard Stark” books.
Kerr Avon from Blake’s Seven, naturally.
Oh yeah.
Also, HIM !
From comics:
Grendel (Hunter Rose)
The Shade (from Starman)
Jesse Custer (from Preacher)
Catwoman (only Ed Brubaker’s version)
Grifter (from Wildcats and Point Blank)
Holden Carver (from Sleeper)
John Constantine (from Hellblazer)
From movies:
Clarence and Alabama Worley (from True Romance)
Jules Winfield (from Pulp Fiction)
CAPTAIN Jack Sparrow (from Pirates of the Caribbean)
Martin Blank (from Grosse Pointe Blank)
Bud White, Ed Exley, and Jack Vincennes (from L.A. Confidential)
Tyler Durden and The Narrator (from Fight Club)
Agent Sands (from Once Upon A Time In Mexico)
Porter (from Payback)
From TV:
Jack Bauer (from 24)
Vic Mackey and everyone else from The Shield
I kinda thought Gollum was the antihero protagonist of Peter Jackson’s The Two Towers. Am I the only one?
I’ll add another vote for The Dude and ask if Yossarian counts?
You’re not. Gollum, books and movies, is the very definition of anti-hero.
In no particular order:
Jack Burton - Big Trouble in Little China
Snake Pliskin - Escape From NY
El Mariachi - Desperado
Jack Bauer - 24
Jules - Pulp Fiction
Tyler Durden - Fight Club
Dirty Harry/Man w No Name/Clint Eastwood - Good, Bad and the Ugly and a dozen westerns (he’s always the same character…punk)
Ash - Evil Dead movies
Scarface
Han Solo (pre Greedo shooting first)
This long and no mention of Raymond Chandler’s Philip Marlowe? One of my favorite characters of all, antihero or otherwise.
Then of course there’s **Gully Foyle ** from Alfred Bester’s The Stars My Destination. That boy wanted him some revenge. “Vorga I kill you filthy!”
another vote for Alex DeLarge
Count Dracula
Peter Cushing’s portrayal of Victor Frankenstein
two Vincent Price characters- Dr. Anton Phibes and Edward (Theatre of Blood) Lionheart
and Lord Summerisle (The Wicker Man)
What, nobody’s mentioned Richard III yet?
In a vague sort or order…
Victor Franko (Dirty Dozen)
Mr. Pink
John Constantine
Louis Mazzini (Kind Hearts and Coronets)
Yossarian
The Good, The Bad and The Ugly
Grimjack
I agree that Hannibal Lecter is not the protagonist in Red Dragon or Silence of the Lambs, but he is in Hannibal. Lecter is the main character (along with Clarice Starling—but the book was named after him), and the main villian is Mason Verger. You end up liking him despite his being a serial killer because he ends up killing characters that you dislike even more.
The McManus Brothers, Top of my list
Not quite sure if he qualifies, but Vic Sage/The Question
Izzy O’Toole (from the Question)
Alex DeLarge
Batman (Darknight Returns version)
Captain Jack Sparrow
Peace - DESK
I forgot Johnny in Mike Leigh’s Naked
And Tom Ripley…as played by John Malkovitch not that other guy! in Ripley’s Game, not the one that did get a US release :(. (I can’t comment on the books.)
Barry Lyndon – from the book and the movie! In both, he’s an opportunistic sonofabitch, but you still want him to win. One thing I noticed: He’s much, much more of a sonofabitch in the book, but the effect is much the same. My theory: Kubrick couldn’t make him that horrible and still keep a movie audience’s sympathy, because a book reader, putting more time and effort into constructing an imagined world, is readier than a movie viewer to sympathize or identify with a POV character.
Jack “Hacksaw” Bauer from 24 is clearly a hero, not an anti-hero. Sure, he’s a hero who plays by his own rules, but imho, he’s absolutely a hero.
So is Mavra Chang, by the way.
Hear, hear! Mad Science forever!
I’m not sure you can really call him an anti-hero.
After all, he crippled a bunch of childern to make money. That’s more what a villian would do.
Garrett, from the Thief games is a personal favorite of mine. He’s not Robin Hood, or any other likable rogue with a heart of gold. He doesn’t steal from the rich and give to the poor–he steals from the rich and pays his rent. He’s cynical, opportunistic, and downright antisocial. The nicest thing he’s done is blackjack some people so the fiance of one of his few friends could sneak out to elope (while stealing a wedding gift from the same house).
Nevertheless, he’s saved the city from a murderous cult and killed a destructive deity. Of course, he mostly did it because they annoyed him…
I suppose it doesn’t hurt that his internal monologues sound a hell of a lot like mine. 
I’m going to have to agree that Gollum is no hero. He may be a protagonist, but villains can be that as well, and that’s precisely what he is. Sure, at some point he does start to fall more in line with his happy go lucky “Hibbitses are our friends” type mentality, but up to the very end, he’s really being ruled by his own jealousy and greed and hunger for the ring. He has no intent on destroying it, but keeping it for himself. Virtually every step he took on the voyage with Frodo and Sam was for his own greedy little benefit and not that of the greater good. He “destroyed” the ring by accidentaly falling into a volcano…not a heroic act by any means.
Most of mine have been named, but Guts from the manga/anime Berserk is by far one of the coolest bastards I’ve ever known. He’s on a quest to kill a ring of evil demons, but isn’t afraid of running through entire villages to get there, or leading innocent little children and their grandfathers to horrible deaths by undead.
Hell Tanner in Damnation Alley.
All of the three lead cops in LA Confidential
Peter Bondurant of *American Tabloid and another couple of James Ellroy novels.
Chili Palmer of Get Shorty
John Shaft of Shaft
Mike Hammer of a million Spillane books
Hawk of the Spencer series by Robert Parker
Butch and Sundance
Tyler from Fight Club
Jay Gatsby of The Great GatsbyMad Max
Alex in A Clockwork Orange