There are still some Marvel universe characters that don't belongs to Marvel what movie rights are concerned. Spider-Man, Hulk and probably Namor. But there are other titles outside the Marvel universe as well.
Present:
Malibu Comics. Plenty of characters and titles, especially in the Ultraverse.
Men in Black
Red Sonja. I don't think Marvel has the rights, despite being a created by Roy Thomas and Barry Windsor-Smith.
Past:
Transformers
ROM: Spaceknight
Micronauts
Any titles not mentioned?