My humble opinions in no particular order:
50.
49.
48.
47.
46.
45.
44.
43.
42.
41.
40. Brak from "Space Ghost"
39. Brain from "Pinky & the Brain"
38. The Grinch from "How the Grinch Stole Christmas"
37. Lucy from "Charlie Brown"
36. Zoltar from "Battle of the Planets"
35. Bobby's older siblings from "Bobby's World"
34. The Decepticons from "Transformers"
33. Wilma's mother from "The Flintstones"
32. Mr. Buzzcut from "Beavis & Butt-head"
31. Kahn from "King of the Hill"
30. Shredder from "Teenage Mutant Ninja Turtles"
29. Commander Feral from "SWAT Kats: The Radical Squadron"
28. Scrappy Doo from "Scooby Doo"-Scrappy techinically, was one of the good guys, but a lot of the fans absolutely hate him anyway.
27. Prince Lotor from "Voltron, Defender of the Universe"
26. Mum-Ra from "Thundercats"
25. Dr. Zen from "Johnny Quest"
24. Gargamale from "Smurfs"
23. King Chicken from "Duckman"
22. Mojo-Jojo from "The Powerpuff Girls"
21. George Liquor from "Ren & Stimpy"
20. Yosemite Sam from "Looney Toons"
19. Snidley Whiplash from "Dudley Do-Right"
18. Dasterdly & Muttley from "Wacky Races"
17. Mr. Slate from "The Flintstones"
16. Dr. Claw from "Inspector Gadget"
15. The Joker from "Batman: The Animated Series"
14. Zorak from "Space Ghost"
13. Bluto from "Popeye"
12. The Legion of Doom from "Superfriends"
11. Mr. McVicker from "Beavis & Butt-head"
10. Boris & Nastasha from "The Adventures of Rocky & Bullwinkle"
9. Roger from "Doug"
8. Angelica from "Rugrats"
7. Mr. Spacely from "The Jetsons"
6. Skeletor from "He-Man"
5. Cobra Commander from "GI Joe"
4. Stewie from "Family Guy"
3. Cartman from "South Park"
2. Mr. Burns from "The Simpsons"
1. Sideshow Bob from "The Simpsons"

When AFI did their list for the top 50 heroes & villains in movie history, the only animated characters that made the list were the Queen from "Snow White", Cruella DeVille from "101 Dalmations", and "Man" from "Bambi."

Comic Book Resources Forums > Miscellaneous Forums > TV/Film > Rank The Top 50 Greatest Animated Villains In TV History (http://forums.comicbookresources.com/showthread.php?s=&threadid=94224&perpage=15&pagenumber=1)

Well, how about a few less than 50? #10- Tom of Tom and Jerry( Who said a villain can't be loveable ? ) #9- Mr Spacely #8-Catwoman ( too sexy to omit ) #7- Boris Badinoff and Natasha ( the team Rocket of the 60s ) #6- Dilandau ( the totally insane male princess of Escaflowne ) #5- Bluto ( or Brutus , same guy , more or less...long story ) #4- The Joker #3- Peg Leg Pete ( AKA Black and Sneaky Pete ...Mickey Mouse's evil cat enemy ) #2- Naraku ( A demon from Inuyasha whos goal in life is to make everyone suffer ) and, the #1 villain on my list, Dr. Ikari from Evangelion ( An evil scientist who makes his only son a pawn in his twisted plot to replace mankind with his own creations )