This is as much as I can remember after plowing through the Wikipedia cartoon listings to jog my memory.
Classic: Bugs Bunny appears to be anatomically correct when he's wrapping the towel around himself in "The Wabbit Who Came to Dinner." Naked cherubs and Bare Mountain zombie women in Fantasia. Droopy and his donkey at the tail end of that sheep vs cows one.
Silver Age Warners: Hampton loses his overalls and has to streak home in "Bacon Strip." Randy Beamon's pal did two stories in a towel, which fell off both times, showing his butt once and almost showing his, um, boyhood in another. The New Year's Baby on Histeria! had some diaperless moments.
Silver Age other: Bobby's World, I vaguely remember Bobby getting mad because they were laughing at his bare butt, but I don't remember the butt. I know there was something on Gargoyles but my mind froze - Demona turned into a human, maybe? I haven't thought about these shows in forever.
Cartoon Network: Dex about a zillion times. The Eds in their premiere and a zillion other times, Johnny 2x4 was "feeling the breeze" once, and I think Jimmy's in there too, but I'm not certain. Billy about a zillion times. The Mayor of Townsville in "The Bare Facts" and I'd swear the girls were once but my mind's gone blank. Nigel Uno losing his bathers and coming home naked, The Tommy in the tub. I think Courage when the nauuuughty guy shaved him, been a while since I saw that. Good call on "Kenny and the Chimp." Also the original "Mike, Lu and Og" short, Og had no backflap on his loincloth. Mac on a sugar high in "Sweet Soiree," Eduardo after Bloo shaves him in "Land of the Flea," Madame Foster as a nature girl in "Camp Keep," most of the friends go nude anyhow. Adam Lyon videotaped in the shower a couple of weeks ago on the monkey butt show. I'm counting the monkey himself and also Cow and Chicken for the realistic rears of everybody in it, and the endless string of pork butts they ate.
Nickelodeon: Ren and Stimpy. All the Rugrats except Angelica, I don't think she ever did. Rocko charged a nude beach looking for his dog and was in an experimental film without his knowledge (Naaaaaa-keeeeed!) and maybe Heffer lost his pants once but I can't be sure. The Flesh. Donnie Thornberry in flashbacks to his life with the orangutan mom. SpongeBob in "Hooky" and "I'm Your Biggest Fanatic," Squidward in the one where Pearl takes over the restaurant, Patrick I know but I can't remember in what. Timmy Turner zapped out of the bath, and I think he also did a lost bathers scene, also Cosmo air-bathing for no reason I can remember. Truman X on the toilet a week or two ago after he built his own Tiny House.
Simpsons: Homer, Marge, Bart, Maggie. Lisa? Mr Burns. Groundskeeper Willie. Nelson Prince. Martin Prince. Clinton and Dole. Who hasn't been naked on that show? Just toss in Fry on Futurama and McFarlane's stuff too. Drawn Together and whatever that other show is on Comedy Central.
Anime: MYYY BRRAAAIIN HURRRRTSSS.