This has been on multi-decade, on-going debate for a while now. Everybody has there opinion, but there is no right or wrong answer. Below I've listed the iconic/moreso famous heroes and villains from each company respectively. (Keep in mind, the list is not in order of importance, and yes I know they are more, but I was just too lazy to do it).
(Heroes)
1] Spider-Man
2] Captain America
3] Thor
4] Iron Man
5] The Hulk
6] Wolverine
7] Silver Surfer
8] Daredevil
9] Ghost Rider
10] Avengers
11] Fantastic Four
12] X-Men
13] Ghost Rider
14] Namor
15] Dr. Strange
(Villains)
1] Dr.Doom
2] Magneto
3] Galactus
4] Thanos
5] Green Goblin
6] Apocalypse
7] Brotherhood of Evil Mutants
8] Venom
9] Mephisto
10] Juggernaut
11] Red Skull
12] Hydra
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(Heroes)
1] Superman
2] Batman
3] Wonder Woman
4] The Flash
5] Green Lantern
6] Aquaman
7] Captain Marvel
8] Martian Manhunter
9] Robin
10] Nightwing
11] Justice League of America
12] Justice Society of America
13] Teen Titans
14] Hawkman
15] Dr. Fate
(Villains)
1] Lex Luthor
2] The Joker
3] Darkseid
4] Catwoman
5] Ra's Al Ghul
6] Deathstroke
7] Mr. Freeze
8] Doomsday
9] Sinestro
10] Mongul