In the character videos in F-Zero GX, Antonio Guster and Blood Falcon strip down to their boxers (camouflage and pink with teddy bears!, respectively) while doing their laundry. In Captain Falcon's video, he splits his pants while saving a baby, revealing red polka-dots.
Wario himself has trouble keeping his pants up on the map screen.
In the Metal Slug series, the Prisoners Of War reward you for rescuing them by pulling a giant pair of blue-and-white-striped boxers out of their pants and dispensing an item from them.
Also, when the Mars People betray General Morden in Metal Slug 2/X and 3, they strip him to his undies. In 2/X, they're pink bikini briefs; in 3, polka-dot shorts.
Agent Smith in the Hitman games is often seen wearing boxer shorts printed with the US Flag.
While merchandise and cameos often depict Arthur as wearing heart boxers (as noted above), official artwork has always put strawberries on his boxers instead. In Ultimate Ghosts 'n Goblins, these strawberries were visible in-game for the first time.
In Marvel vs. Capcom 3, every one of Arthur's costumes gives him different boxers, with strawberries as the default. His alternates are blue and white vertical stripes, green with white polka dots, and gold with black stars.
Arthur wears vertically striped boxers in the obscure Wonderswan game (which also appear in one of his alternate outfits in MvC3).
As mentioned above, Maximo can acquire a variety of different boxers in his games, including monogrammed, cow-spotted, and dollar signs. In the second game, each print gives a different bonus.
In RosenkreuzStilette Freudenstachel, Grolla's heavily Ghosts 'n Goblins-themed stage includes Skeletal Knights that resemble Arthur, including armor that breaks off in one hit and strawberry-print boxers.
While monsters in Dragon Quest VIII don't wave any about when they do the move, Yangus pulls out two pairs of blue-and-white striped boxers when he performs the Underpants Dance move. For understandable reasons, this causes the Confusion status ailment.
Spyro: A Hero's Tail has Gnasty Gnorc reveal his red polka-dot boxers when he's goaded into swinging so hard that his staff/club sticks into the ground. More humiliating is the fact that this is his weak point.
In Normality, Norm 2782 is left in his polka-dot boxers after protagonist Kent Knudson takes his uniform for a disguise (and doesn't give it back when he's done with it). Norm 2782 finally gets his clothes back in the ending cutscene.
Most of the male vampires in Akiba's Trip are wearing some sort of patterned underwear.
In Kid Icarus: Uprising, the enemy called Erinus is a cloaked figure that splits into two when it takes enough damage. The upper half keeps the cloak, while the lower half is left in pink striped boxers.
Disgaea 5: We don't actually see them, but Red Magnus has a pair of tiger-print briefs that are his favorite (and only good) pair of underwear. Seraphina is not amused when he puts them in with her laundry.
The Final Boss of Smash TV combines Mutoid Man (the first boss) with the M.C. of the game show. Rather than exposing his ribcage (as with Mutoid Man previously), shooting his chest reveals a pink polka dot undershirt.
As mentioned before, in a WarioWare game, you must defend yourself from a ninja. Well, on the easy difficulty, the ninja costume falls off to reveal boxers. On the medium difficulty, the boxers fall off to reveal briefs. And on the third difficulty... the ninja is wearing a pink thong. Really.