Excalibur's Genoshan member Freakshow covers himself with a stop sign after demorphing from his monster form the first time we see it. (However, he still has underwear, which doesn't really make sense... and is unnecessary, because of the stop sign.)
That's a trope itself in Marvel Comics (Exiles did it nigh-constantly)... Characters who've had their clothing destroyed will regularly be shown in underwear — usually underwear at least as modest as some teammates' outerwear — yet have dialog indicating they're stark naked. Yeah, there's a history of Marvel editors realizing that, ye gods, there's too much flesh, and demanding the artists put the character in Y-fronts or a one-piece.
In Secret Six, they first encounter the Mad Hatter sitting on a throne of skulls wearing nothing but a hat over his genitals. Turns out, it wasn't just to cover them.
Red Hood spends part of Issue 6 of Red Hood and the Outlaws completely naked, walking about using his hands and a palm leaf to cover himself, along with bandages on his torso after his clothes get destroyed. Could also double as Naked People Are Funny.
Plastique was seen trying to cover her crotch with her hands after Firestorm stripped her naked by de-atomizing her clothes to get the bombs she was carrying - much to the amusement of her would be victims.
There was a man who saw a lake and decided to go swimming on a hot day. He didn't have a bathing suit, but since he was alone, he took his clothes off and jumped right in. Suddenly, he heard female voices and giggling, and quickly covered up with the nearest object he could find: an old discarded bucket by the shore. "Hello, ladies," he said, rather embarrassed. "You know, I can read minds," one of the women said. "You can?" asked the embarrassed man. "Yes," she replied. "You're thinking that old bucket has a bottom."
A vicar was entertaining a visiting bishop, and the two decided to go swimming in the nearby lake. They had no swimwear, but decided it wouldn't matter since there was no-one in the vicinity. After awhile a group of women from the village suddenly appeared, and the vicar quickly covered his nether regions with his hands and ran to his clothes in the bushes. The bishop did the same, but instead covered his face. When the vicar asked why he hadn't covered his privates, the bishop answered: "Most people recognise me by the face".