There are quite a few gay super-heroes running around nowadays, but very few gay super-villains... in terms of out characters, I can only think of Man-Killer and Machinesmith. Letha and Lascivious (female villains from The Grapplers), seemed to have a romantic pairing in the Punisher Annual a few years ago, yet recently in Avengers Undercover, they rock-paper-scissored for Chase Stein's attention. Poundcakes also was hinted at being a lesbian in Women of Marvel, yet she came on a bit strong to the Beast in A+X. Other than that, Daken is bisexual, and now apparently Loki is, as well. Who else?
I personally have always thought of Blizzard as gay, as in Nicieza's Thunderbolts run, he seemed to chase Speed Demon around like a lovesick puppy. But Nicieza even remarked that he never intended Blizzard to be such (though he could see why others thought so).
List of GLBT Marvel Super Villains:
Andreas von Strucker - bisexual
Daken - bisexual
Destiny - lesbian/bisexual
Electro - bisexual
Lascivious - bisexual(?)
Letha - bisexual (?)
Loki - bisexual
Machinesmith - gay
Man-Killer - lesbian
Mindmeld - transgender
Mystique - bisexual
Purple Man - bisexual
Poundcakes - bisexual(?)
Shinobi Shaw - bisexual
Skein - bisexual
Superia - lesbian