Yuuto is the only male in Aselia the Eternal - The Spirit of Eternity Sword that could really be described as pretty. On the other hand, he's also pretty muscular by the end, so despite the face, he isn't exactly girly.
Sergei from Asura's Wrath. Yasha is to an extent too, though not quite as much.
Bayonetta 2: The Masked Lumen is an androgynous-looking man under his mask, with flowing, waist length platinum blonde hair, narrow eyes, thin lips, smooth pale skin, and a slender build. The impressive thing is you can tell he's one when just a sliver of his mask gets knocked off, revealing only one of his eyes and the general shape of his features around it. Balderwas quite a looker when he was younger.
Alucard is one of the quintessential examples. Though mistaking him for a girl is not likely to be a problem, though, given the loving attention put into his sprite and the fact that his VA has a very, very deep voice. Ironically Alucard from his debut game Castlevania III: Dracula's Curse was as far from Bishie you can get, it wasn't till the non-canon Castlevania Legends that Alucard got a prettier design◊ which likely served as the basis for his iconic Castlevania: Symphony of the Nightbishōnen look◊.
Ayami Kojima who did most of the later artwork for Castlevania really, reallyloves this trope to point where she’s responsible for turningevery single male protagonist (and even Dracula) into a bishōnen. The only exception being Julius Belmont who is older and rugged.
Dante much like Leon from Resident Evil (who he was based on) just barely makes the list because while Dante is a very handsome dude (especially in DMC3 and DMC4) he's still very masculine and even a outright Hunk in his Shirtless Scene, plus he gets Perma-Stubble. At point in the third game Dante even admires himself in the reflection of his sword and both Nevan and Morrigan call him a "handsome devil". The anime plays this much straighter◊ with Dante compared to the games.
Vergil Dante's Evil Twin is pretty bishie since he's identical to his brother (especially with his hair down◊), though other games such as Project × Zone make this trope more pronounced. Other games and artwork downplay this like Dante making more masculine and dignified. Ironically, both Dante and Vergil subvert the Bishounen Line as their respective Devil Triggers make them far less pretty than their base forms.
Nero plays this straighter than Dante and Vergil being very androgynous◊ and even more so in the pachinko game◊. Averted in DMC5 where in line with the game realistic art style Nero is more masculine, though ironically Nero's Devil trigger in the game is closer being bishōnen than Dante and Veril's DTs being a hybrid of Long-Haired Pretty Boy and Gorgeous Gorgon.
Quite a few male characters in the Disgaea series, including (but not limited to) Mid-boss, Seraph Lamington, Fukubei, Master Big star, Adell, and Tink.
In Dragon Quest XI, the main playable character, the Luminary, has long hair and noticeably finer features than previous heroes in the series, and is frequently noted to be handsome and even beautiful by various characters throughout the game. More than one female NPC comments on wanting looks like his.
Dynasty Warriors has its fair share, with Jin (Sima Yi, Sima Shi, Sima Zhao, Zhong Hui, Xiahou Ba, Jia Chong, Wen Yang) being a certified Cast Full of Pretty Boys. The other kingdoms don't fail to deliver however with Shu (Zhao Yun, Jiang Wei, Guan Suo, Guan Xing, Zhang Bao), Wu (Zhou Yu, Lu Xun, Ling Tong), and especially Wei (Zhang He, Cao Pi, Guo Jia) hosting some impressive examples.
Many of the characters of Eternal Sonata are well-noted for this, including the game's main character Frederic Chopin and the main on-screen avatar character, Allegretto.
Final Fantasy series: any of the main male characters, at least once graphics became advanced enough to portray it; the official character art shows that the older ones actually were this, too, when not depicted with blocky, low-resolution sprites. Specifically:
Sephiroth. In the original cut of the scene with Sephiroth frozen in crystalized Mako, he was to have feminine curves to allude back to Jenova. Things were scaled back there for the same reason Squall in VIII was made to look more masculine.
As for Kuja from Final Fantasy IX, he reaches truly Dude Looks Like a Lady proportions. This is even Lampshaded by Queen Brahne, who outright calls him a "girly-man". To be fair, though, he calls her "elephant-lady".
The page-top quote refers to Noel Kreiss, one of two playable characters (outside of DLC) in Final Fantasy XIII-2. A popular theory is that his character design is based on early designs of Fang from Final Fantasy XIII when she was a male character. Whether or not it's true, his pretty boy looks fit the trope to a tee.
And then there's Vayne Solidor of Final Fantasy XII, who even in full armor is still a very slender guy with more hair than two out of the three women in the main party.
Regarding Noctis from Final Fantasy XV, he is normally bishōnen, but after the timeskip, he starts sporting a Manly Facial Hair and looks far more rugged, but once he's clean-shaven it's shown he's still as pretty as ever.
Lucius, the amazingly feminine featured pretty boy monk with long blond hair. Of course, he defends the fact that he is male when confronted by Serra.
A typical Fire Emblem game will have several bishōnen, at least a couple of rugged manly men, a few good looking grandpas, and a Gonk or two. Few are as bafflingly pretty as Lucius, though.
When Super Smash Bros. first showed off Marth, most western players were initially quite confused as to whether Marth was a girl or not (hairband and girly name didn't help) . His voice actor cleared this up a bit, though.
Less so than Libra, but the default, Type 01 build for a male Robin is fairly bishōnen, especially if you give him long hair.
Fire Emblem Fates: Kaze, Jakob, and especiallyLeo and Takumi all have soft, pretty features. Leo's son Forrest takes it to a whole other level. Azura's son, Shigure, qualifies as well, and his finer features are exaggerated further in his Cipher cards. The default male 1 build for Corrin as well.
Fire Emblem Echoes: Shadows of Valentia has several, some of which are due to the art having improved from the original. Tobin and Kliff both have soft, pretty faces in the remake, and are fairly slender to boot. Luthier and Leon are the long-haired variety; Leon is said to have a strict routine to keep himself looking nice, and it's accentuated by the fact that he appears to be wearing eyeshadow and lip gloss.
Fire Emblem: Three Houses has four stand out examples. From least to most bishie there's Jeritza, who's frame is wide enough to offset his pretty face and long hair, Male Byleth, who's about on par with Marth in terms of prettiness, Linhardt, who has long hair and slender body to compliment his pretty face, and Yuri, who, similar to Leon above, appears to be wearing eyeliner and lip gloss, in addition to having long hair.
Granblue Fantasy has multiple examples, in part thanks to its huge cast. Most notable perhaps are Joel and Summer Albert, both of whom also double as Mr. Fanservice thanks to outfits which reveal a lot of skin (especially abs).
Grumpy rival farmer Jamie from Harvest Moon: Magical Melody is a bishōnen or a bifauxnen depending on what gender you play as. If you play as Amanda, he is a secret bachelor but the game ends if you marry him.
Skye is the "special" bachelor from Harvest Moon DS and is sometimes regarded as the turning point where the series began making more bishōnen characters. He is a Gentleman Thief that is prone to Bishie Sparkles.
Similarly, many of the young males in the spinoff series Rune Factory are bishōnen. The protagonist of Rune Factory 4 barely looks male, which, what with the Hello, [Insert Name Here] nature of the game, can lead to some unintentionally hilarious moments:
"Sophie? What a fine, manly name!"
Harvest Town, a game that is inspired by the above Harvest Moon, features a number of attractive bachelors. The most obvious example is Lee Yau, the Hospital Hottie whose initial character design looks more like a model than a doctor, and Duke Evans, a suave musician who looks like a typical "popular guy" from a shoujo manga (especially his newer character art). There's also Chris Ford, who isn't explicitly said to be handsome by the in-game bio, but is drawn in a similar enough style with the two aforementioned examples, that it's impossible for him not to qualify.
Among the attractive male characters in Infinite Space, a few of them fall into bishōnen/biseinen category. Lord Roth is arguably the best example, with his waist-length lavender hair and feminine face. Main character Yuri is quite pretty himself.
Link becomes even prettier in The Legend of Zelda: Breath of the Wild, to the point where characters of both sexes feel attraction to and openly flirt with Link. Sure, it's been implied in previous entries to the series, but it has never been this blatant. This actually helps Link in one main quest where he has to dress up like a Gerudo in order to get into the female-only town they reside in.
Magna Carta: Tears of Blood kicks the bishōnen up to 11, making its main lead, Calintz, and his apprentice, Azel, almost entirely unrecognizable as male. Chris Arcway manages to dodge the bullet with his open button-up shirt and cocky womanizing attitude, but even Raul, the tall, masculine, goateed swordsman who appears a few times in the game, gets a touch of Bishie thanks to the artstyle (no matter how impossible it seems to be Bishie with a goatee).
Raiden in Metal Gear Solid 2: Sons of Liberty was designed as an androgynous hero who Kojima created after hearing two teenage girls complaining that military games are full of old men. In the game there’s even a scene where another character makes a grab for his groin, and is surprised to find he is male. And you have to play as him naked. No, we are not making that up. He was widely reviled for this by the fans, among other reasons. Eventually, Raiden's own game, Metal Gear Rising: Revengeance, buffed him up◊ to the extreme.
The Japanese iPhone/Android game My Horse Prince is a Dating Sim about a young woman named Umako meeting the handsome Yuuma on a ranch. Seems like a normal enough game until you learn that Yuuma is a horse with a human head and the game still plays with some Dating Sim tropes despite its weird love interest.
Pretty much any guy from the NeoRomance series (Angelique, Harukanaru Toki no Naka de, La Corda d'Oro). Eisen of Haruka proved to be pretty enough to disguise himself as a girl on one occasion; even the Emperor is bishōnen, though he has the excuse of being Eisen's half-brother. In the La Corda d'Oro anime, one character (Kenichi Shimizu) actually gets called a bishōnen by the lead girl when she first meets him.
Odin Sphere: Prince Cornelius of Titania, the Shadow Knight Oswald, and Prince Ingway of Valentine. All three young men's physical features (well, in Cornelius and Ingway's human forms, anyway) fit the archetypes of handsome princes and brave knights with slender yet muscular builds. In Ingway's case, his outfit even runs into Mr. Fanservice territory.
Ōkami has Waka, who FLIES seemingly by virtue of sheer Bishie Sparkle and his improbable headdress.
Bishōnen characters in other games include Falkner, Bugsy, Morty, Will, Wallace, Steven, Roark, Volkner, Riley, Aaron, Lucian, and Marlon. Maxie may count as well, even though he's older than the others.
The male player characters have been trending toward this in Gens 5 and 6. Calem, the male player character for X and Y, is probably the most blatant example - especially when compared to Red's original game design. Or for previous gens, compare the remake design of Red to his to original one.
As of Pokémon Sun and Moon, Red no longer qualifies, instead showing signs of maturing into a Hunk. On the other hand, his rival Blue is edging much more into this now, though granted he had been showing signs of this since HeartGold/SoulSilver
Leon S. Kennedy makes the cut, but barely. Even at his prettiest, he was still quite solidly built and masculine, and his face becomes a little more chiseled and tough-looking in each new appearance. His haircut, though, remains top-shelf bishōnen.
Steve Burnside from Resident Evil – Code: Veronica plays this trope straighter than Leon, not being very masculine at all. But subverted as you won’t find many Steve fangirls since he’s considered The Scrappy of Code Veronica being incredibly annoying and whiny.
From the same game Albert Ashford is so androgynous he can disguise himself as his twin sister, Alexia. He's even accused of being a transvestite.
Even Chris Redfield (thanks to the art style) is turned into a bishōnen◊ in Code Veronica contrasting to other games where he’s depicted as a rugged Hunk.
Interestingly William Birkin was originally conceived as one◊ of these in Resident Evil 2 but later games retcon him into being more scraggly looking, which is more in line with his Mad Scientist character.
Akihiko Sanada from is a borderline example; he's a tall and lean Chick Magnet, but he's also a boxer with a noticeably masculine physique.
In a less obvious manner, the main character may also qualify, having a very slender figure, subtle facial features, and pretty eyes. He's also frequently described as a "pretty boy" or "handsome", to the point where a certain Corrupt Corporate Executive tries to exploit him.
Both Goro Akechi and Yusuke Kitagawa are definitely this, both being attractive young men with slender, elegant features. Goro's Thief outfit is even that of a prince's.
The protagonist from is definitely a bishōnen. Between his looks, outfit, voice, and attitude (bonus points for his evil panty-dropping smirk), he's definitely got a devoted female fanbase and more than a few fanboys. Joker's probably the prettiest Persona protagonist, and is by far the sexiest.
Samurai Warriors: we have Mitsuhide, Hanbei, Ranmaru, Kiyomasa, Motochika, and Kojiro.
Keiji is a strange case, as he has a muscular figure but a very pretty face and long, silky hair. And Yukimura also seems to become more feminine looking with each new installment.
Ramirez from Skies of Arcadia seems to rock the "pretty but misunderstood" vibe as hard as he possibly can. Enrique is pretty much his good counterpart. A number of recruitable crew members further the bishōnen appeal, particularly Lawrence and Ilchymis.
Vega is a narcissist who believes his face to be extremely beautiful, and cannot stand the ugly. Part of it comes from traumatization as a child when his ugly father killed his beautiful mother. He also wears a mask, not to hide his identity, but to prevent his face from being scarred. Evil Makes You Ugly is often invoked for Vega, as several World Warriors point out in their win quotes.
Remy in Street Fighter III is even more of one (though he's not narcissistic like Vega).
In the Alpha series, Ken becomes one of these, with long, flowing hair in a ponytail and a younger face (some pieces of art◊ for the game even show him with pronounced lips, a rarity for Street Fighter characters). However, the other games show him looking older and more muscular, with Perma-Stubble.
The Suikoden series of games have, quite literally, dozens of bishōnen among the ranks of the Stars of Destiny (108 per game!). Notable ones include and are not limited to: every main protagonist, Flik, Luc and Sasarai, and Yuber.
In the Super Smash Bros. games, characters of this nature (e.g. Pit, Shulk, Cloud) tend to have all-female crowd cheers.
Although having more of a fairly (and by that, we mean in the smallest margin, as the game models differ slightly from the official art) masculine face than some other Tales Series bishōnen, Richard from Tales of Graces certainly fits the role, having traditional elements including medium-length blond hair, fancy frilly clothes, and immense popularity throughout the kingdom (in one skit, he mentions his "dilemma" with the sale of Richard-themed items). His seiyuu is even the same as a certain other bishōnen of Tsubasa -RESERVoir CHRoNiCLE-, and he even sports ZelosWilder's costume as DLC. Doesn't help that his younger self can be seriously mistaken for a girl.
Zelos from Tales of Symphonia. Yggdrasil, too. Some fans would argue that Kratos is one as well. The game is ripe with bishies. Kratos is a good example of a biseinen, or 'beautiful man' - what a bishōnen becomes when he grows up.
Several of the guys in Tales of Vesperia: particularly Yuri, who can be mistaken for a woman until he opens his mouth.
The Trails Series has its fair share of this, but special mention goes to Prince Olivert Reise Arnor, who is fully aware of it and plays it for all it's worth. He'll flirt with anyone he can and his other tropes include the Bishie Sparkle and Say It with Hearts. There's also Kurt Vander, whose pretty-boy look is regularly commented upon and early on in Cold Steel IV is mistaken for a girl by a little girl NPC.
WarioWare has Young Cricket. In a game where every male character is either ugly or goofy-looking, Young Cricket stands out by looking like a handsome young man.
In World of Warcraft many of the other characters say Blood Elf males (particularly those without facial hair) are this, verging on Dude Looks Like a Lady. However, this is part of the setting's Fantastic Racism: their actual design is a lot more Hunky than the in-game dialog would suggest. Night Elf and Nightbourne males deliberately invoke this trope, since the women are dominant in their societies: so looking feminine means looking powerful.
Zandalari troll males tend towards this from a troll perspective. Unlike other trolls, among the Zandalari the males aren't much bigger than the females. Both sexes can be bald or otherwise have similar hairstyles, and facial hair is uncommon among trolls generally. Therefore, telling the sex of a Zandalari-especially in armor-can be difficult. Zandalari males do still have the longer tusks typical of male trolls, but this characteristic can be obscured by helmets.