Ned Beatty was truly despicable in Shooter (2007) playing a 'John McCain-esque' U.S. Senator. Come to think of it, Danny Glover had a particularly nasty part in that film as well.
Jason Isaacs - The Patriot, Harry Potter films, and other notable bad guy roles in other films Tim Roth - Reservoir Dogs, Rob Roy, Planet of the Apes (remake), etc.
Stephen Graham in This Is England. - Probably the most convincing acting I have ever seen. Ben Foster in 3:10 to Yuma - He must have had a blast playing this role.
Powers Boothe - Sudden Death, Blue Sky, Tombstone Van Heflin - Possessed, The Prowler Ann Baxter - All About Eve, Guest in the House Everett McGill - People Under the Stairs, Silver Bullet, Under Siege 2 William Shatner - The Intruder Chris Sarandon - Fright Night William Forsythe - lots of stuff Laird Cregar - only in the biz for 4 years before dying but many great baddie roles Gary Busey - Surviving the Game, Under Siege (his son is a good baddie too) Humphrey Bogart - Brother Orchid, Conflict, Two Mrs. Carrolls (always preferred him as a heavy.) His best villain was 1992's Diggstown. So despicable he got actual death threats.
I might have missed her in this thread but there's Louise Fletcher as Nurse Ratched in One Flew Over the Cuckoo's Nest.
Bruce Dern, in the 1972 John Wayne film The Cowboys. When he breaks the kid's glasses ... oooh, what a bastard.
Ow man, so many good ones! How to choose? Gary Oldman in (Leon) The Professional Samuel L. Jackson in Django Unchained
But he played a great "can't wait to see his comeuppance" villain in Witchfinder General. A part he played perfectly straight, and how could you camp up such a despicable real life villain anyway? Basil Rathbone deserves a shout out for the times he played a snobbish sword fighting prince/king.
Powers Boothe also played a really sadistic bastard on Deadwood, and was effectively creepy as 'The Rev' in Guyana Tragedy: The Story of Jim Jones (1980)