My list:
1. Joker: Owned the movie. He totally overwhelmed a very good Michael Keaton.
2. Zod: Loved how he had this disinterested, totally blaise attitude about taking over and ruling the world.
3. Lex Luthor: Campy yes, but still very formidable.
4. Magneto: He hasn't really been allowed to cut loose, but McKellan has the bearing, the majesty that captures Magneto almost perfectly.
5. Green Goblin: Doesn't get the credit he deserves, but he was a more dangerous, personal foe for Spidey than Ock.
6. Deacon Frost: Hip and arrogant. He matched up well with Blade, while making vampires cool again in the process.
7. Nomak: Loved the Reapers, and him. Nomak was an unstoppable force, and I loved the family drama thing too.
8. Ra's Al Ghul: A little too understated for my taste, but I still think overall Neeson pulled it off. I could definitely see him leading the League of Shadows, much more than the other guy.
9. Howard Saint: One of Travolta's best performances. Saint was a thoroughly believable villian, with a simple motivation.
10. Top Dollar: Put him on the list, because he, and his 'sister' Myca really creeped me out when I first saw this film.
Honorable Mentions:
I liked David Banner, Doc Ock, Mystique, Dr. Doom, Lady Deathstrike, Stryker, Scarecrow, and Kingpin, but particularly in the cases of Scarecrow and Kingpin, I didn't see enough of them to put them on a top ten list.
Mystique was pretty much the sexy muscle of Magneto in the X-Films. Stryker was somewhat run of the mill, but still well acted. David Banner was creepy. Dr. Doom was underplayed, but I know McMahon has a great Doom performance in him. Doc Ock is overrated in Spidey 2, but still a pretty good villian.