Possibly the two most prolific villains in comic history but who you think takes the cake as the greatest villain in all comics, not talking powers wise but motivations, quotes and just sheer awesomeness.
@Joygirl: Same, no matter how powerful Darkseid is I still am far more scared of the Joker particularly after reading Killing Joke. The images of Jason writhing on the floor from death in the family also brought chills as it was so real and hideous, plus clowns creep the hell out of me.
Magneto back in his day was the best kind of villain for me. He had a purpose, he had a real goal. As horrible as his conquest was, in his mind he was doing the right thing. He was caught on one end of a two sided battle and demanded war. He had a drastic means to obtain the same goals the X-Men fought for really, and it was almost tragic that the two had to fight each other.
The Joker was always awesome because he never really had any other goal than to torment and cause chaos/havoc. To me the same reasons he is awesome are the same reasons I can't read too much of him at a time. He satisfies the need to read a true villain, some so completely malevolent that there is no line between good and evil, because he is truly evil.
However, I personally prefer comics that operate much more in the morally gray area. I like to read villains who just barely nudge the line between good and evil. Who fight for the same goals and ideals you would expect any person to fight for, and someone who uses their personal, and political power to obtain them. While on the other end you have a hero who has more in common with their foe than they have differences. To me this makes a villain whom one can identify with to some degree, and that's what really makes them good to read. They aren't so over the top evil that you can necessarily place the "evil" tag on them so easily, and to some degree you can identify with their self loathing when their plans inevitably succumb to failure.
These are the same reasons I prefer Marvel over DC actually. I love reading characters like the Joker, Hank Henshaw, Sinestro, Thanos, and Loki. However, I prefer morally gray characters and stories like John Constantine, The Creeper, X-Men (in general), the Watchmen, Frank Castle, Ultimate Marvel, etc.
I know, kind of a long response, but I'm not exactly known for my short-windedness I guess.
Thanks for reading,
@Floopay: You shouldn't apologize that was an amazing reply and one I completely agree with :D
However I'd personally place Sinestro in the morally grey area as his motives of protecting his race remind me somewhat of Magneto
@moywar700: True sometimes what you need is a true malevolent force that makes you truly scared for the hero, a problem with morally grey villains is that sometimes you risk rooting more for the villain than the hero :)