Sir Arthur's traditional garb in Ghosts N Goblins once his armor breaks (though according to official artwork, they're strawberries — see below). In one game, he switches instead to long johns.
Tatsunoko Vs Capcom is the only game in which he's clearly wearing heart boxers in the in-game graphics.
The Spiritual SuccessorMaximo: Ghosts to Glory also has heart boxers as part of the game-long Homage, with other prints available for purchase. The sequel, Maximo Versus the Army Of Zin, expands this, giving the title character the ability to change boxers to get additional powers (like the ability to get an extra level of armor).
In Kings Quest VII, the Werebear is left in these after jackalope!Valanice blows off his fur and pants.
In Quest For Glory II, while sleeping at the Inn in Raseir, the hero can be seen wearing these when his blanket is pulled off by a rat.
In Wario Ware: Smooth Moves, one of the missions has Wario defend himself from a ninja. You must slash at the right time to tear off the ninja's suit. But wait, there's more... (scroll down...)
In Spyro the Dragon, the large Gnorcs in Gnorc Cove who defend themselves with barrels are left in these and a tank top after you blow their clothes off.
In Rocket Knight Adventures (and the recent 2.5D revival, Rocket Knight), these seem to be part of the uniform for the pig soldiers of the Devotindos Empire.
In Mickey Mania, the final boss Pete wears these (just like in the cartoon the level is based on). The dagger-throwing weasel guards in the same level wear pink polka dots instead.
In Punch-Out Wii, King Hippo has upgraded to star-print boxers.
The Soviet Premier in the Allied ending of Red Alert 2 is found hiding under a desk wearing boxers with a red "Hammer and sickle" print motif (He had dressed a decoy in his uniform).
In the character videos in F-Zero GX, Antonio Guster and Blood Falcon strip down to their boxers (camouflage and pink with ... something, respectively) when 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.
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.
Which is somewhat odd considering that in his first appearance, he wasn't even wearing pants.
At the end of the first level of Plok, Plok finds a pair of polka-dot boxers instead of the flag he was looking for.
Other men's underwear
The mini-boss Jukid in Kirby Super Star is wearing polka-dot . . . underwear of some sort. It's hard to get more specific since he has no legs.
The Bokoblins in The Legend of Zelda: Skyward Sword have a predilection for "fashionable undergarments" . . . "fashionable" here meaning leopard print.
As mentioned before, in a Wario Ware 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 pink panties. Really.
They're never shown, but it's confirmed by Juliet herself in Lollipop Chainsaw that she's wearing her 'lucky zombie-fighting underwear', which is panties with teddy bears or hearts on them.
