Dr. Doom - the greatest villain of all time, IMO.
Mr. Sinister - a joke now, but like what pointed out before he used to be incredible as a villain
Bullseye - I love when he's not portrayed as a complete psycho and actually given some depth. Gruenwald, Bendis, Brubaker, and Way have all handled him masterfully
Morlun - easily my favorite new villain of the past decade, JMS made a pretty generic concept interesting
Magneto - I haven't considered him a true villain since I entered double digits of age, but I guess he should be on here
Nimrod - he has one of the coolest designs in robot history
Mirror Master - there should be a law Grant Morrison has to write an ongoing series with him
.... that's all I can think of off the top of my head.