I'll just do a top 3 for each:
Sympathetic
To me, a sympathetic villain is one whose motivations are understandable and I get why they've become a monster.
1. Magneto, most villains suffer trauma, but Magneto's experiences during the holocaust are probably among the worst of any comic book character. His goals and methods have become terribly twisted, but at least we can understand why he is the way he is.
2.General Zod, again twisted goals and methods but an understandable villain because he was following his programming and protecting his people (similar to Magneto in some ways). I really enjoyed Shannon's portrayal (which only gets better in light of Jessie Eisenberg's Lex Luthor). Interestingly, I find Terrence Stamp's Zod to be the opposite, a completely unsympathetic villain.
3. Zemo, who embodies the " dig two graves " notion of revenge. The fact that he's just human, and while skilled not incredibly exceptional, and has a very understandable grudge against the Avengers make him quite a sympathetic villain. I think Zemo is the best villain we've seen in years actually, because he's so different (than the typical cackling evil masterminds) and unassuming.
Oh, and honourable mention to Catwoman in Batman returns.
Unsympathetic
1. The Joker (in pretty much every incarnation) but best epitomized by Heath Ledger in TDK. Honorable mention to Harvey Dent, I think he should have got a movie to himself, but oh well.
2. Loki, sure he has daddy issues, but that's it. Don't get me wrong, he's a great villain - not too far behind Ledger's Joker - but he's really just a spoiled brat. The "Puny God" moment in the Avengers, has to be one of the top moments in comic book films.
3. Ronan the Accuser. Thanos' "pouty child " comment was right on the mark. He was a monomaniacal genocidal lunatic, who was willing to sacrifice everything and everyone around him just to destroy Xandar. What an ******* !
Honourable mention
Not to subvert what's already a great fun thread, but I propose a third category:
"villains you cheered for.....when they DIED ! "
Sebastian Shaw, when Magneto pushes the coin through his head, I cheered !
Kevin Bacon made him charming but utterly detestable.
Bane, TDKR, couldn't wait for him to get offed. I suppose it was the fact that he maimed Batman, and then after Batman kicked his ash and was only stopped from beating on him some more by a stab in the back, was an utterly graceless winner by immediately putting a gun in Bats' face - to me that's just terrible form. Cheered when he got blown away.
Ultron, was highly looking forward to his robotic demise. He was underdeveloped and really needed more screentime and lines to really make an impression. But Spader made him unlikeable enough that I was very pleased when he finally got offed.
Ronan (although I mentioned him above) would have fallen into this category too, as I cheered when the Guardians blew him to smithereens.