Man, I love villains as far as stories go. A lame villain can really ruin a movie, since in movies that utilize a villain, the villain sets the tone and pace of everything. I'll post photos since you wanted that.
The Joker- Because he's completely insane and unpredictable, and confuses even other villains, and Ledger's interpretation was phenomenal. He's not driven by the typical emotions of greed or power like most villains, he "just wants to see the world burn". So, Batman and others have no idea how to stop someone who has no reasonable motive.
Magneto- Because he's a deep villain. Sometimes he is interpreted as an anti hero rather than a villain, whereas other times he is so cold-hearted he is clearly a villain. His best friend is Xavier, his enemy/rival, who he respects dearly. As a young man, he was a Jew imprisoned in a death camp in the Holocaust, and survived. Now as a mutant, he sees the same discrimination and fear of mutants, so he strikes back hard against humans to protect mutants.
Darkseid- Because he's basically the "final" villain for things superman-related. He was the final villain for the last season of smallville, the final villain for Justice League Unlimited, etc. He's stronger than superman, has an army, and is very intelligent and manipulative. He's basically an ancient demigod. (Picture shows him in the back, with Supergirl in the front.)
Legato- A bad guy from Trigun. His character differs between the anime and manga, and I like the anime version. He was sort of the secondary bad guy, but his personality made him mostly the primary villain. He's completely calm and exceptionally evil, and his final plan is extremely dark and creative.
Vincent Volaju- from the Cowboy Bebop movie. He was a soldier driven insane, and now is delusional and wants to end the world. He doesn't feel pain, and is very cold and calm.
The Operative- The unnamed primary villain of the movie Serenity. He is cold and calm at all times, and very smart. He's interesting because he honorably fights for what he thinks is the right thing, and yet is the villain. For a villain he has an oddly selfless motive- he is trying to build a better world, and is removing people that don't belong in that world, and admits that this includes himself because he does such evil things for its purpose. "I'm a monster. What I do is evil. I have no illusions about it, but it must be done."