Metal Gear Solid 2 had Raiden, and even stripped him naked near the end of the game. It's also fair to note that Snake's outfit suddenly and inexplicably got very, very tight. Particularly around the buttocks. The character designer freely admitted that Raiden was to appeal to girls who liked handsome young Bishōnen, and Snake to girls who liked sexy older men.
Raiden was even intended to have visible panty lines under his suit, but, in the most recent figurine line, Raiden's underwear is nowhere to be seen - and Snake's underwear lines are incredibly visible over his stupidly well-sculpted buttocks, probably as a nod to the fact that Snake unintentionally became more popular with the girls than Raiden.
Liquid Snake. Blond, British, wanders around shirtless in Alaska.
Don't forget Bridget, who's become quite popular amongst fangirls.
While every male character in BlazBlue is attractively designed, the biggest fangirl baits in the game are Jin and Hazama. Jin is a tsundere bishounen with tight clothing and troubled past. A sexy pillowcase featuring him sold at twice the amount of Noel's and Rachel's pillowcases weeks before it was even designed. Hazama, the smooth criminal, is a very well dressed troll who dances as he fights. He is the only character, male or female, who has a bath scene in game.
Tales of Vesperia: Yuri Lowell, anyone? His outfits had built in chest exposure. Some of his alternate outfits (especially in the Japanese PS3 version) involve showing a fair bit of skin, or have him in skin-tight outfits.
Mass Effect: The game's enormous female following is largely due to the ability to play a female Shepard, but in case that wasn't enough incentive...
Most of the male love interests are some degree of Mr. Fanservice, but Thane takes the cake: the assassin seeking redemption with a troubled past, deep raspy voice, a taste for leather, and a tendency to show off a good portion of his pecs (mind you, that's to help stave off a terminal disease, but still). He was specifically designed by the creators to provide a male counterpart to the asari.
James Vega takes up the mantle in the third game. He's not a romance option, but the game doesn't mind letting players admire his body, in and out of universe.
Vagrant Story has have Ashley in his assless battleshorts, muscle-revealing shirtfront, and improbable red hair, or the shirtless Sydney with his barely-hanging-on pants and dramatic buttcape.
Devil May Cry with Dante, courtesy of his shirtless younger self just stepping out of the shower in the first scene of the third game. It runs in the family: see his older twin Vergil and nephew Nero.
Persona 3 has Akihiko Sanada, a white haired Bishōnen who is totally adorable. He gets a couple of shirtless scenes in the game: the Beach Episode where he walks out on the beach in nothing but a speedo, and the hot springs episode where he is once again lacking in the clothes department. In Persona 3: FES and Persona 3 Portable, you can actually have him wear his bathing suit to Tartarus, though he keeps a shirt on. In Persona 3 Portable if you play as the female protagonist, she can have a romantic relationship with him — you even go to his room and "spend a long time with him" when you max his S.Link.
The main character from Shin Megami Tensei III: Nocturne spends 98% of the time shirtless. It's practically a shirtless game. The only time the Demi-Fiend wears a shirt is in the prologue (the first 30-60 minutes of a ~50 hour game), before there's any actual gameplay. He's pretty buff, too.
The Prince manages to lose more and more of his upper-body clothes over the course of the first game, until he's completely shirtless.
Kaim from Lost Odyssey has very formfitting armour, with a nice sliver of flesh that shows off his hips and lower back. Not to mention the scene when he awakes after losing his memories, and is shirtless.
Final Fantasy VIII has Squall and Irvine. Irvine was specifically designed to be less attractive than Squall, who was based on a popular J Pop artist. The former is brooding, snarky, with a Dark and Troubled Past, and the latter is a carefree and highly flirtatious cowboy.
Final Fantasy XII gives us Balthier, the dashing, handsome pirate rogue whose mostly there for the same reason Fran is: the eye candy.
The male Blood Elf player character in World of Warcraft could qualify as this, appearing in the game at about the same time Blizzard began to realize they had a significant female playerbase.
At the very least, his original model was pretty enough that the male fans set up a howling outcry until the developers bulked up his muscles. He still has much more delicate facial features and much more fabulous hair options than any of the other male models.
The Suikoden games all have a pair of combination attacks ("Pretty Boy(s)" and "Fancy Lad(s)") where that game's collection of bishonen gang up to attack the enemy. Needless to say, there's usually at least one who qualifies for this trope.
The Dark Tales series gives this role to Poe's master detective C. Auguste Dupin. He's tall, well-built, and well-dressed, with bright blue eyes and a pleasant voice that always comments about how happy he is to see you.
While very few of the male characters in Mortal Kombatseem to be able to find a shirt, Johnny Cage, with his literally constant bare-chestedness and passes at the ladies, seems to be the one intended to appeal to female players.