Thanos:
Has the infinity gauntlet, which gives him total control over all of reality.
Immortality
Invulnerability to even adamantium, the strongest substance on earth.
Super strength.
Darkseid:
Omega beams: just insanely powerful and injure you to the brink of death, and don't stop until they hit their target.
Immortality.
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Thanatos was kind of annoying villain and his story just sort of died when you beat him. Hades is a much, much better villain in that game. Darkseed was a really weird point-and-click game, but I loved the H.R Gieger inspired visuals, as well as the dark and bizarre storyline.