Hans Gruber from Die Hard. Such a fun villain!
But yes also to Lex from Smallville.
Does Hannibal Lector count?
The Mayor from Buffy and Crowley from Supernatural don't count, IMO, because those shows had some great protagonists, too and the villain, no matter how fun, didn't really 'steal the show.'
Solid examples already given.
I firmly will repeat Gul Dukat on DS9!! Garak may be the closest to an anti-hero on the show also, loved Garak centered stories. His role for In the Pale Moonlight is exceptional!!
Recently for me it was Batwoman. Rachel Skarsten's character of Alice was much better than the title lead in any season.
"Freedom is the right of all sentient beings" - Optimus Prime
M3gan, arguably any batman movie. Except for BvS.
Pretty much any slasher movie since those are based on the villain rather than the hero(es).
Star Wars (pretty much all the movies)
Collateral (Tom Cruise)
Dungeons & Dragons cartoon (Venger)
The Dark Knight
Boyd Crowder was half the reason Justified was so awesome
Definitely, my next choice would be...
Amon
I'm slightly surprised that nobody's yet mentioned Babylon 5's Alfred Bester. Sure Koenig chewed the scenery, but it was a delight to watch.
I'd mention G'Kar and Londo, but their arcs were too complex for a simple villain label.
B5MindWar.jpg
So many 'villains' were so layered in that show. It was easy to see G'Kar as the bad-guy in season 1, then Londo in later seasons, and Bester for much of his run, but it's hard to identify them as 100% villain, even if Londo and Bester were both pretty great as villains. (G'Kar face-turned early, not so much 'no longer a villain' but being so ruthlessly treated by the bigger badder villain(s) as to earn some sympathy.)
Mr. Morden and President Santiago seem the closest to two-dimensional villains the show got. And comeuppance was had, satisfyingly.