I like a lot of different comics, although I definitely skew towards DC. Marvel is good, but DC has better villains overall. Some of my favorites are neither. Here we go.
DC:
Heroes - Martian Manhunter, Wonder Woman, Hawkgirl, Green Lanterns (Pretty much all of them), Superman
Anti-heroes - Batman (Yes, I think he is more of an anti-hero), Nightwing, Sinestro, Poison Ivy, Ras al-Ghul
Villains - Scarecrow, Joker, Atrocitus, Larfleeze, Darkseid
Marvel:
Heroes - Spider-man, Storm, Beast, Falcon, Nightcrawler
Anti-heroes - Daredevil, Deadpool, Magneto, Archangel, Venom
Villains - Carnage, Apocalypse, Dark Beast, Sinister, Doctor Octopus
Miscellaneous (Image, Dark Horse, DC - Vertigo (If this is the characters primary storyline), etc.)
Heroes - Animal Man, Hellboy, Abe Sapien, Swamp Thing, Johann Kraus
Anti-heroes - Spawn, Constantine, Dream, Death, Lucifer
Villains - Rasputin, Kroenen, Malebolgia, Violator, Hecate