Wow - first up amazing listing - and those that thought of other ones that aren't on the list is great too.
My list.
10. The Phalanx/The Brood - to me they are tied because they basically do the same thing as far villains go. They're the borg of the MU. Assimulate others.
9. The Neo - too new but had loads of potential. Mostly because of wanting to survive and protect themselves. The were a quiet villain with their own beliefs.
8. Bastion - he's complex and has agendas with agendas.
7. Apocalypse - his background with his lapses in time makes him hard to put any lower on the list but what he can do when he's awake is formidable. Sort of like Godzilla. He does his bad stuff then takes a nap. (Only Godzilla is cooler, imo).
6. Shadow King - he mind controls people and while not my favorite thing to happen to a character, if done right can be compelling.
5. Vargus - the whole rich, money aspect and being so self serving - puts him in a level of villain that is compelling to me. Its more than being bad, its being rich and bad.
4. Dark Phoenix - problem with this villain is they really aren't that much different from the Phalanx and Brood - but ... the real difference is power and loads of it. How it corrupts the person in possession is probably the most interesting thing about it.
3. Onslaught - because no one expected Onslaught - origins and all. And the character was so unexpected that is one of the appealing things about the character. He is unexpected.
2. Magneto - not much to say about him. The fact he believes what he does and doesn't back down says it all.
1. Sinister - his scientific agenda for whatever reason, makes him more vile because he lacks the care or ethics outside of his own. It's not that he's obsessed with power or anything more than that, but its really imo - just for his own curiosity enjoys the benefits that come with it.
Okay - for those who don't want to make a list, pick a villain and discuss the villain or discuss other thoughts here in the villain arena.