Wolverine was shown wearing such underpants, when he tried to go through airport security, but his adamantium skeleton kept setting off the metal detectors.
The Riddler apparently has green question-mark print boxers.
Deadpool is occasionally seen in boxers with his logo (a stylized version of his mask) on them.
He's also occasionally seen in boxers featuring other heroes' logos, including Captain America. One gag featured him upset that his Squirrel Girl Underoos(TM) were improperly washed. That's right, Squirrel Girl. Might explain why she's so vicious towards him.
And to make matters even nuttier, that particular issue happened long before Deadpool even knew that Squirrel Girl even existed. Here at TV Tropes, we like to call this foreshadowing.
His recent adventures take this to a whole new level of horrifying as he has acquired Jean "Marvel Girl" Grey's original costume, complete with tiny yellow panties. An attempt to impress some ladies by stripping down reveals that he wears these when his other clothes are being laundered.
In one Spider-Man story ("Perceptions", where Wolverine guest-starred), Peter wore Felix the Catboxers.◊ (Artist Todd McFarlaine often slipped Felix into the background art, and in this story, where a character actually commented on it, he was scripting the story as well.)
In one Superman story where Mr Mxyzptlk had taken over Metropolis and Superman and Lex Luthor were in an Enemy Mine situation, they attempt to infiltrate "Mxcorp" disguised as guards. Mxy waves a hand to remove their uniforms leaving them in boxers. Supes were blue with an S-shield pattern, and Lex had green with "L"s. (It seems likely Mxy added this touch For the Lulz.)
The cover of the 2000 AD Free Comic Book Day 2014 issue is a parody of the famous image from Spider-Man #50 ("Spider-Man No More!") in which Pete in street clothes walks away from a bin with his Spidey-suit in it. On this cover Judge Dredd is walking away from a re-syk bin containing his Judge uniform, while wearing nothing except boxers printed with his badge.