Sephiroth, the Big Bad of Final Fantasy VII, goes shirtless for the game's final showdown, a one-on-one duel with his nemesis Cloud. Although the low polygon count destroys the point of even bothering with it.
The polygon count was higher in that battle than any of the real ones. Sephiroth also appears "naked but but obscured by something weird from the waist down" in the cutscene where he gains the Black Materia. Which may actually be justified rather than just censorship if you consider his ultimate One-Winged Angel form. Which also had no shirt, but that version really had a tiny polygon count.
The Square Enix store in Japan has a life size statue of Sephiroth frozen in materia set into the floor. Cue drooling
Also, in the prequel Crisis Core, a member of Sephiroth's fanclub mentions how much she'd like to see him "stripped to the waist."
And then there's Zack's shirtless beach scene in Crisis Core, complete with invisible armour and materia slots.
On the other hand, if the PS3 remake of FFVII ever comes to fruition, that shirtless fight scene will be rendered with today's hyper-realistic graphics. Damn.
Sephiroth goes shirtless in his alt costume in Dissidia. Careful not to drool on your PSP.
Sephiroth also goes shirtless in his alt costume in Ehrgeiz: God Bless the Ring. Rendered better than in FFVII, but obviously not as good as Dissidia.
In similar fashion, the first Kingdom Hearts game's Final Boss also goes shirtless after he somehow merged with a gargantuan Heartless battleship for the final battle of the game.
Both he and Sephiroth wear trenchcoats with no shirt underneath (though Sephiroth wears what looks like a leather daddy harness), making every scene a shirtless scene for them. Their final boss forms just take it a step farther.
On the side of good, Sora does as the natives do when in Atlantica and loses the shirt along with his legs when he becomes a merman. It's the one redeeming point of said level.
Ventus is, for some reason, shirtless in his Awakening. It becomes Squick when you realize that Master Xehanort is the one who probably undressed him, and he was about eleven.
The boys of Final Fantasy X, save for Auron, don't need shirts or armor to ward off magic attacks or bladed implements! Oddly enough, the most dressed guy is the undead one, for all the good proper equipment did him!
An especially odd-looking case is Seymour, who wears some sort of robe that is open almost to his crotch, displaying some very bizarre and unsexy tattoos, although this is just the icing on the cake to some.
The sequel also gives us Brother, who never wears a shirt, and an optional scene features shirtless Buddy getting a massage from a Hypello.
Who gets the hyper-detailed rendering mentioned above, and has random freckles, moles, little bumps on his aerolas and erect nipples. Oh, Square, you cocktease.
Devil May Cry 3: Dante's Awakening begins with Dante shirtless and just coming out of the shower. He remains shirtless for the first stage, and you can unlock an alternate costume that lets you play the entire game with this character model.
The title character from Prince of Persia: The Sands of Time begins the game fully dressed and apparently wearing some sort of leather armour. As the game progresses, his clothing is torn off or used for bandages bit by bit until he is just wearing his pants.
Additionally, the bulk of The Two Thrones is just one long shirtless scene.
At the end of Metal Gear Solid, Liquid — who spends most of the game wandering around, outside, without a shirt, in the middle of Alaska — removes Solid Snake's shirt. This is because Snake's padded sneaking suit functions as armor, maybe not so much to bullets but certainly against hands and feet.
Metal Gear Solid 3: Snake Eater gives the player the option to take Naked Snake's shirt off at any time for no reason at all (you're even penalised for doing it, since it increases Snake's stamina-drain rate and reduces his resistance to colds, parasites, and bullets). The player does get a funny line or two about it when Snake puts in a call on his radio while half-naked.
In Metal Gear Solid 4, Snake does a Fan DisserviceShirtless Scene for Naomi. (Un)fortunately, even wrinkled skin, liver spots, Ugly Pants, unflattering lighting, sad music and Naomi being moved to tears by his ugliness really did not counter the fact that he still has a killer figure. Possibly intentional, knowing the director.
Metal Gear Solid: Portable Ops had Big Boss do like Raiden and get stripped completely naked by his captors. Unfortunately, thanks to the sketchy art style of the cutscenes, you can't make out much.
He also has shirtless scenes (with pants on) in the beginning and ending.
Grand Theft Auto: San Andreas gives players the option to dress CJ however they wish... that includes stripping him to his underpants for a nearly completely nude shootout with cops and rival gangsters! Is the block hot or is it just me?
The players can dress characters of either gender in The Elder Scrolls III: Morrowind in whatever they please or in as little as they please...and I do mean whatever! (Okay, so human females get the perma-bra treatment there.) The hero can take down Big Bad Dagoth Ur in nothing but a gauntlet and what look to be burlap undies. Now that's mightiness!
In fact, Dagoth Ur himself doesn't wear much other than a loincloth and an Aztec mask. Again, though, the low polygon count detracts from the Fanservice.
Don't forget everyone's favorite improbably ripped old bald guy, Caius Cosades.
In Dreamfall: The Longest Journey, the very first look the player gets of Kian the Apostle is in a Shirtless Scene pitting him against other burly shirtless men. Note that only the playable male character is introduced this way. Zoe is in her underpants, though.
In the Bloody Roar games, several fighters go shirtless. For the furries (talking only about Beast forms from here on), Yugo and Gado go shirtless in most (all, in Gado's case) of their costumes in the first game. Yugo has an open vest in Beast form in the second game, but still no shirt, and Beast form Bakuryu goes shirtless. Gado keeps his clothes on, however. After the second game, Yugo keeps his clothes on, but Shenlong now goes shirtless, and Reiji, who's shirtless in both Human AND Beast forms, comes into play.
The Krauser boss fight in Resident Evil 4. At the start of the battle, he is wearing only a bandolier (on account of Leon slicing a bit of his shirt open in an earlier cutscene, and him inexplicably opting to ditch the said shirt as opposed to bearing with the tiny tear), and as the fight progresses, he ends up losing the bandolier for no real reason as well. Basically, the whole fight is a strip show.
There is also a brief gratuitous shirtless Wesker scene in Resident Evil 5 in the last boss battle against him, albeit his bare chest is overcome by the gross tendrils of the Uroburous virus a few seconds thereafter.
Fire Emblem: Radiant Dawn has a nice, lengthy Shirtless Scene during a flashback sequence from one of the last characters one would have expected to get one. The Black Knight a.k.a. Zelgius, who also surprisingly turns out to be quite a Bishonen under all of that armor.
Not to mention Volug, who, due to the wonder of static portraits, is essentially shirtless throughout the entire game. The fact that he's a mysterious loner and a wolf-man makes it easy to see why the series' female fans swoon over him. Just look at him.◊
Waking up after Ostagar (though you don't see much).
Imprisoned in Fort Drakon.
In the Gauntlet. (In all three cases, the women are in bra and panties and the men are in undies...though Oghren in his underoos is definitely Fan Disservice.
Sadly averted in the sequel though, unless you strip your male Hawke. Though you do get to see the female equivalent of Merrill in a corset if you romance her...
Well, temporarily in Brain Dead 13: If Lance can't make a choice of either a shave, manicure or facial quick enough, Vivi will quickly hold his head to her side and pull down both his spider web barber cloth and his shirt, exposing not just his neck, but also his bare chest and his man nipples (!), before taking a bite and draining him of blood!
Garcia begins Shadows of the Damned shirtless, grabbing his leather jacket just before he jumps into the portal to Hell.
If you could actually count this as a game, then there's John in the beginning scene of Plumbers Don't Wear Ties, right up until he gets on his motorcycle.
The developers of the PC series Dark Tales announced in advance that in the fifth game, Mr. Fanservice Auguste Dupin would have a shirtless scene. The fangirls rejoiced. Unfortunately, what they didn't announce was that said shirtless scene would come at the cost of Dupin being shot in the chest, and the player character has to cut away the shirt in order to tend the wound. He does get better, though, and he's got what looks like a nice build under his Victorian fashion sense.