Point to note: Even thought most of them have debuted in the movies, I am using their comic references and taking in account only those comics which I have collected.
2. Lex Luthor
Genius, ex-president, criminal mastermind, businessman, sociopath. Lex does not have any super power, but still gives a tough time to the big boy blue (a phrase he refers to Superman). He has superior intellect and is pure ruthless among other things. When he was finally beaten and broke, he carried a cryptonite in his pocket for years waiting for chance to kill superman.
Joker misses the top three slot in my list, only because of Mutants and Gods, other than that Joker is completely mad.
5. Dr. Doom
He is nearly as genius as Lex Luthor, add to that the power of the dark arts and black magic, Victor Von Doom is one hell of a villain. The ruler of Latveria is one of Marvel comic’s greatest foes. He is the primary enemy for Mr. Fantastic (Reed Richards) and will stop at nothing to see him dead and humiliated.
The maniacal, powerful parasitic alien is one of the most feared super-villains in Spider-man. Venom is not a person, but a parasitic creature in the form of a black costume, which attaches itself to the wearer enhancing the senses and strength of the host.
Darkseid is a God from the DC Universe, he is not as powerful as Galactus, but if we have to compare him with Marvel universe, he is strong equivalent to Thanos (The arch-enemy of silver surfer and the lover of Death, his rank is 11th in the list of super-villains)
8. Ra's al Ghul
How can one forget, the immortal one? When I say immortal, I literally mean immortal. Ra’s has lived for an incredibly long time, beating death with the use of his Lazarus Pit. His incredible intelligence and abilities in martial arts and swordsmanship makes Ra’s a formidable opponent, worthy the title of super villain.
9. Green Goblin
En Sabah Nur (The First One in Arabic) is one of the early mutant in the world. He is born in Egypt during the First Dynasty (around 3000 BC) and abandoned by the then world who knew no mutants. For a complete millennium he has traveled the world seeking things which will empower him making him the most powerful mutants of all time.
The only problem about this villain, I don't like is the character, its too loud. His first messenger, Mesmero, was much more frighting with the hooded tattooed face than him.