Solaris. Best underused villain ever. I mean, what's a better foe for Superman than a giant, intelligent and evil sun? Absolutely great character with a great origin story. Sad that the only person who gets to use him is Grant Morrison. But with Grant on Action right now I hope to see him again.
Maxima is great if she still counts as a villain. I love her motivation. It's twisted in a crazy stalker way but you can sort of see her reasoning, and any time you can relate to a villain, its good. I hope to see her return in the New52, without going soft like she did in the League.
Manchester Black is a personal favorite but I really dont know if I can call him one of the best. Maybe? He just didnt show up a lot. But he does get major points for everything he did to Clark after Our Worlds At War. Few people have been able to hurt Clark like Black did.
Same sort of goes for Conduit. I liked the character but he just didnt hang long enough to get the level of cred he needs to be called one of the greats.
Ignition is the same, only to a lesser extent. I wish something had been done with him as I thought he had a great visual and an intriguing history (saved from the Emperor Joker reality) but DC never did anything with him.
And then, there's Hank Henshaw. Cant wait to see him again. I thought Johns did a great job building on what Death&Return set up, and honestly, him stealing the character for GL will only make the next Superman/Henshaw run-in that much more epic. Assuming the character still exists. With Clark's death and past being sort of murky, Im not sure how that works with Sinestro Corps War, which certainly still happened in continuity.
So I guess its Henshaw and Solaris for me.