Yukiteru is seen in his underwear one last time in episode 23, where he strips nude so the Doctor can administer some device or potion to make him taller, so he can better impress the girl he likes. She walks in on this however, and in the end she just thinks he's a pervert.
Episode 17 has the boys in their underwear for health inspection day.
In episode 5 of Dokkiri Doctor, Yukihiro gets his hands on one of the Doctor's inventions, a helmet which changes the wearer's personality. The machines a bit buggy however, and Yukihiro ends up doing a strip tease in front of his mortified teacher and running throughout the school in his briefs.
In "Parasite", suggestive pictures of Robin show up on his computer.
In "Ghostboy" Beast Boy melvins himself much to Starfite's disgust.
In the episode "Nature", Beast Boy tries to re-connect with nature by throwing off his clothes (sans underwear) and living in the wilds. Submitted by MrAnimeopera.
If anyone else knows of other Teen Titans Go! underwear scenes let me know and I'll screen cap them.
There's a quick shot of Beast Boy in briefs in the episode "Real Magic". Submitted by MrAnimeopera.
Beast Boy is seen in briefs in "Laundry Day", where the Titans' clothes turn against them. Last screenshot submitted by MrAnimeopera.
Robin is seen briefly in his underwear in the episode "Dude Relax".