Okay, so the "Have you tried not being a mutant" scene from X-Men 2 was pretty squirm-inducing (in a good way). But when it comes to uncomfortable "coming out" scenes in superhero movies, you can't really beat this moment from Disney's Sky High. In which the dad — Kurt Russell! — gets so pissed he practically smashes the table and then pulverizes a phone.
Sky High, like a lot of movies and TV shows about superheroes, tends to focus on the trappings of the genre, perhaps at the expense of the substance of the genre. Although it still does manage to be fun and occasionally actually pretty winsome. In Sky High, the son of two superheroes (Michael Angarano) goes to a special superhero high school. (High point: the gym teacher is Bruce Campbell. Also, the principal is Lynda Carter.)
And for some sadistic, godforsaken reason, the school separates the kids into heroes and sidekicks, which is partly just an excuse for lots of jokes about the cliches of superhero comics and television from the 1950s and 1960s. (Sidekicks learn to say "Holy ______" and the like.) But it's also a commentary, in true Disney fashion, on the whole idea of separating kids into jocks and nerds, or popular kids and losers. Blah blah blah.
But because of the many layers of weirdness embedded in the whole "sidekick" archetype, you get a few scenes like the one above, where "sidekick" is like something you need to come out as. And the scene where Kurt Russell's former sidekick, American Boy (News Radio's Dave Foley), is teaching sidekick studies at the school, and he introduces himself — I shit you not — as Mr. Boy. And keeps commenting on stuff like how the old red-white-and-blue uniform brought out his eyes. Holy Frederic Wertham!