Soo, what are we going on then? The degree of darkness in their hearts or the cruelty they have actually committed? If the former, well, Darkseid is considered a "god of evil" in the DC universe. Nothing he does is for good, only to serve himself. If the latter, well, Cassidy has killed his thousands, Darkseid has killed his billions, if not more.
As far as the aforementioned breakdown goes, even Thanos has at one point sought redemption (hell, I have the tpb titled: "Thanos: Redemption"). Darkseid would never do that.
But, can't help it now :p Thanos is tied with DS as my favorite villain, so...he still gets my vote.
My favorite is Joker...but this is just a terrible set of options. Where's Darkseid, Galactus, Sinestro, Bane, Doctor Doom, Professor Zoom, Riddler, Ra's Al Ghul, Deathstroke, The Rogues, Doomsday, Two-Face, Scarecrow, Parallax, or about a thousand others?
Tough choice between Magneto & Venom, ultimately I chose Magneto. He's not your stereotypical villain, which is why I like him and consider him to be the greatest of all time. He's always upheld a certain code of honor, which seems rare with villains these days. He had a vision for a world fit for Mutants, which he chose to pursue, mostly in a rather villainous way, but in his mind, was the righteous way.