My favorite pairings that aren't mentioned:
Clark Kent and Lex Luthor, especially in Smallville. Because hoboy I've seen farmboys crushing on each other and trying desperately to make it not so, and it looked very much like that. If the boys I knew could've wrecked a planet between them in superpowered romantic death throes, they would've done it. Clark and Lex's doomed relationship is well founded on their location: if you're bisexual in a small town, you're better off chasing girls.
Professor X and Magneto, deliciously played up in X-Men: First Class, hinted at in various other incarnations including a couple of cartoons. Most tellingly, they'll threaten each other all day ... but if you make a credible threat against one and the other finds out, bend over and kiss your ass goodbye. Charles and Erik are very much products of their time. When Erik comes from, being queer got you killed. Charles may be more optimistic, but he's not much less stuffy. It's the love that dares not speak its name.
Okay, over to you. Who do you think should come out of the closet?