I don't know if anime would count or not (since DBZ and Pokemon have already appeared, I'm guessing so).
5: Apocalypse (The X-Men)- The only villain in any cartoon series dangerous enough for other villains in the
series to join in the fight against. He didn't have an army of mutants at his command. He didn't mass produce
giant robots to aid him. He didn't need to.
4: Magneto (The X-Men)- He's a bit higher on the list than Apocalypse simply due to the fact that I really
relate to his ideals. Where Xavier sees a people who hates and fears mutants and says "let's be friends",
Magneto sees a people who hates and fears mutants and says "this is a problem".
3: Vegeta (Dragon Ball Z)- I don't know why, but something about this cocky, arrogant, jerk really grabs my
attention more so than later villains of the series. I guess it's his motivations, his single minded desire to be
the best, not for any reasons of conquest or recognition, but for his own sense of self worth. He even
manages to keep some of his villainous qualities when he face/heel flips so he's a great villain, even after he
stops being a villain. Uniqueness, thy name is Vegeta.
2: Makoto Shishio (Rurouni Kenshin)- Like most on this list, motivation is key. Believing strongly in social darwinism
myself, I was cheering for this guy from beginning to end (even though I knew he'd lose eventually). His goal, to
create a new Japan in which only the fittest survive, not to rule it, but for Japan's own betterment. Is this not
a stand up guy or what?
1: Diva (Blood+)- Again, all about uniqueness and motivation. I won't go into detail on this one, because it's a
massive spoiler. Just go watch it, and you'll see what I mean.