Melfina does the hand thing whenever she's in the tank that lets her navigate the ship on Outlaw Star. The Toonami edit gave her a bikini, which makes this kind of needless.
Tengen Toppa Gurren Lagann: In the Bathhouse Episode, Kamina uses Boota to cover up his naughty bits. In the same episode, Simon's parts are often covered up by his drill, which drops by about a foot and increases in size by a factor of three or so.
Ranma ½: Although Female!Ranma's male mind (and, therefore, complete lack of feminine modesty) make an Innocent Fanservice Girl out of her more times than not, she usually covers her breasts and crotch when in the presence of people she does NOT want to see her naked — such as Kunô, Happôsai, or public bath patrons.
Keiichi, from Higurashi: When They Cry, does this in the pool OVA after he finds out he isn't wearing a swimsuit. Sadly, all four of his friends, a seventeen-year-old, a fifteen-year-old, and two nine-year-olds, saw him for a good half a minute. Two of those girls are his love interests, and one of those two girls fawns over how cute his "sea bear" is.
In a non-comedic example, during "The Second Raid" Kaname is being chased by an assassin while only wearing a robe and her underwear. She distracts said assassin with her removed robe and shoots her with a stun-gun while covering her breasts with her arm.
Episode 11. Taro does it after Ryuuka intrudes into his bath area while he's naked.
Episode 14. Taro, while bathing with Konoe in the natural hot spring.
La Verité episode 1. Taro does it when several maids manage to disrobe him without his knowledge. Several maids (including assistant Security chief Yashima Sanae) do it after one of Ikuyo Suzuki's gadgets rips off their clothing, leaving them naked.
Queen's Blade does this for both tops and bottoms: the ends of Melona's hair form hands that are her only covering for her breasts at any time, and the Elves never wear panties. Alleyne uses leaves for panties, and Echidna uses a live snake.
Bleach anime episode #229. Ikkaku is in the bathroom about to take a bath, with only a towel around his waist. When Keigo's sister walks in, Ikkaku's towel falls to the floor and he has to cover himself with his hands.
In Neon Genesis Evangelion, when Shinji first sees Pen-Pen, he runs out naked into the living room. The only thing blocking his crotch is a can of beer on the table. Shortly after, Misato picks up the can of beer to reveal... a even smaller box of toothpicks. It's at this point she says to Shinji that he forgot his clothes, so he then covers himself with his hands and exits off camera.
The agents of Nudist Beach from Kill la Kill wear only semi-automatic handguns, tactical combat belts, stockings, and sleeves, appropriately enough.
In Midori Days, Seiji uses his hand to cover himself after his sister drops his shorts in front of a crowd . . . forgetting that his hand is a girl named Midori. When he checks on Midori, she's passed out and foaming at the mouth.