Storm Hawks:
In the episode 'The Lesson' Stork tore a small hole in his pants and you could see the pattern of his underwear underneath. They were blue with a skull and crossbone design.
Later in the ep Finn used one of the whips left behind by the raptors on Stork causing his pants to fall down revealing that the skull and crossbone underwear were boxers.
In 'What's Got Into Finn' Stork had his pants pulled off when one of his traps to catch Finn went wrong. He was either wearing the same pair of underwear as before or his underwear consists of numerous pairs of skull and crossbones.
We's seen more (or less as the case was, seeing as he ended up wearing nothing) than underwear in regards to Stork. In Stratosphere he was wearing nothing but a towel and then Radarr pinched it to block a leaking pipe. Stork ended up flying The Condor starkers with strategically placed items blocking his ass and other body parts in that general area.
In 'Talon Academy' Snipe was given a wedgie, he has heart underwear btw and I'm pretty sure he lost his pants entirely in another ep (might have been the same ep, but I can't remember), like Stork he wears boxers
And let's not forget all the Murk Raiders losing their pants (Scabulous made a comment about ginches (Canadian for underwear, I think))
Scabulous - "No, Eyeball, we'll never see our pants again"
There's a fanfic on fanfiction.net where Piper and Dove discuss the underwear preferences of various Sky Knights and villiains. They came to the conclusion that Harrier (stuffy British Sky Knight) wears a thong (I left a review saying that Harrier probably doesn't wear a thong, instead there's a Boratesque mankini under his uniform) and that Repton goes commando.
MASK:
I recall one of the bad guys getting his pants ripped (by a panda, I think) whilst hanging from the bottom of an ascending helicopter, revealing a heart design.