+Anima: Husky. He's repeatedly mistaken for a girl.
Ghost Hunt: almost all of the male characters. Lin, Naru, Bou-san, even John are bishōnens, pretty boys, handsome, etc, etc...you watch a video of Ghost Hunt on YouTube, scroll through the comments, and you will find a lot of fangirling female users.
JoJo's Bizarre Adventure features Noriaki Kakyoin, a VERY popular example on pixiv and possible poster child. Not to mention Part 5 and its collection of dangerous pretty boys.
With the exception of the vampire hunter Toga Yagari, absolutely all the male cast of Vampire Knight are bishōnen.
Reiji from Kodomo no Jikan, especially in the anime. Of course, he's a seriouslyfuckedup bishonen.
Harry from Outlaw Star. He even ties his hair with a big, pretty bow. Fred Luo, too.
Sayonara, Zetsubou-Sensei: Nozomu Itoshiki and his brother Mikoto. Also, four of his only known male students: Jun Kudou, Kuniya Kino, Aoyama, and Haga.
Huey Laforet from Baccano! takes this to the point of confusing people in-universe (you know you look girly when one of the prettiest woman in the series is your nigh-identical adult daughter, and you know you look really girly when you are not mistaken for beautiful women, but beautiful women are mistaken for you). Firo, while never being mistaken for a woman like Huey has, has been mocked by a detective in the Light Novels for skewing quite close to the Uke aesthetic. Claire Stanfield, aka. Rail Tracer, also fits. Jacuzzi also fits, although he has that giant tattoo on his face.
Urusei Yatsura. Rei Lum's (former fiance) is a tall, stoic, green-haired space bishōnen who drives men to despair and women to squee. Mendou also qualifies, which is basically his most obvious difference from Ataru.
Kouichi Hayama, from Moonlight Lady, falls into this description perfectly. Lampshaded with Io Azuma, his wife-to-be's cousin; Suzuna was hoping that Io would grow to be this (partially because of an Arranged Marriage to him). Ultimately averted, as Io grew to be a limp-wristed, wide-eyed, Ambiguously Gay "pretty boy".
Otani, Kohori, Suzuki, Haruka, and, without a doubt, Maitake and Seiko from Lovely Complex.
Just about every male character from Fushigi Yuugi. Most of their brothers from other Yuu Watase manga are bishies as well. It's Yuu Watase, what do you expect?
Dilandau in Vision of Escaflowne(who is later revealed to have been a magically disguised and brainwashed girl). Let's just say that most of the male cast is bishōnen, especially Allen and Van. Just look at the opening, for God's sakes!
The Shitennou in the first season of Sailor Moon, Mamoru Chiba, Ali of the Doom Tree arc, Prince Diamond and Sapphire in Sailor Moon R, the Amazon Trio in Super S, and the Sailor Starlights...sort of. In the manga, even one of the cats qualifies for this with his long haired, midriff exposing human form. The cat in question (Artemis) is even named for a goddess.
The entire male cast of Simoun. The younger men — who were girls until age 17 — even still have breasts that haven't been reabsorbed yet (especially the hunky chief mechanic Wapourif), and all of them are voiced by female voice actors.
Maximilian Jenius from Super Dimension Fortress Macross and Macross7. Also, Linn Kaifun and Conda Bromco from the first series. Justified and repeatedly lampshaded in Macross Frontier with Alto Saotome, who is frequently remarked on for his resemblance to a woman (much to his annoyance). He, and his father, were Kabuki actors who specialised in female performances. Particularly obvious lampshade hanging is his nickname of 'Hime' or 'princess' cause he is just so darn pretty.
Solomon Goldsmith from Blood+. Can't forget tall, dark, and handsome Haji.
Kyuzo in Samurai 7 is tall, slender, and androgynously beautiful; his voice, however, is very male. Shichiroji, too, and Katsushiro is close. Then there is when Gorobei, Heihachi, and Rikichi have to make it to Kanna village... in disguise.
Kousaka from Genshiken. The most feminine-looking male club member, he is the only one with a girlfriend in the beginning, let alone a sex life.
Basically, all male characters from Ouran High School Host Club, and one of the females. Tamaki (see picture) slightly subverts the usual cool-headed bishie stereotype by being a blithering (but lovable) idiot, and manages to be the male lead and comic relief both at once.
Particularly Momiji, Ritsu, and Ayame. The first wears the girls' school uniform (albeit not with a skirt) because "it looks cuter on him", while the second presents himself as a woman because of an inferiority complex the size of Antarctica. Ayame, on the other hand, is...just special. Akito also qualifies in the anime, although manga Akito is a different story altogether.
The lead, Tohru Honda, remarks that the Sohmas are a family of "princes". And towards the end of the manga's run, even Momiji graduates to pure Bishōnen status with a growth spurt and switch to the boy's uniforms.
Gundam Wing, in particular, was full of them. And among the Gundam Wing bishie brigade, Quatre Winner deserves special mention. A slim, platinum-blond Berber. Needless to say, you can find a fairly large amount of fanart of him.
Protagonist Heero Yuy also deserves a mention, since Word of God admitted that his appearance was inspired by a Japanese actress, Yuki Uchida.
Gundam 00, oh ho ho. Apparently, every male under the age of 35 will be absolutely gorgeous in the 24th century, in addition to shrinking their shirts in the dryer to show off their buff figures. Then again, this was pretty well predicted the second they announced that Yun Koga would be designing 00's cast.
Even in the original Mobile Suit Gundam, Char stands out as a pretty boy, notable because the art style of the time rendered almost every other character Gonk. The only character to rival his bishounen-ness is Garma.
Griffith from Berserk is explicitly labeled as "too beautiful to be a man" in about a dozen separate chapters by different characters! He even wears lipstick after transforming into Femto.
Katori, Dom, and the nameless terrorist from the second episode (who is mentioned because his prettiness is a plot point) from Irresponsible Captain Tylor.
Both Ishida Yamato and Ichijouji Ken of Digimon Adventure and Digimon Adventure 02 fall into this category. Their actual looks are never commented upon, but one figures that this is at least partially why they are fangirl bait, both in and out of the show. Also lampshaded in an Audio Drama.
Well, there was that page in the translation of the 02 manga where Daemon calls Ken "the pretty one" (if you're thinking that's too creepy for words, then you're probably still sane).
In one episode of zero two, Gabumon lampshades this by saying "Yamato isn't the only heartthrob here", while Ken was hit on by a very young girl.
To a lesser extent, Takeru, Yamato's little brother, seems to gain some level of bishōnen in him when he turned eleven himself. An episode of Digimon Adventure 02 showed a fair number of girls—Hikari among them—practically swooning over him when he was showing off his basketball skills.
Wolfram is very pretty (he looks almost exactly like his mother), a definite bishōnen. In fact, Yuuri's immediate reaction upon seeing him for the first time is simply to stare in awe and call him exactly that.
Then there's every guy in Yuuri's "harem", plus Yuuri himself.
Johan from Monster. It's especially noticeable when you realize that the anime is one of the few that steers entirely out of the way of Generic Cuteness.
Major Alex Armstrong also appears as a sort of parody, both meeting every bishonen archetype yet defying it too. Not only does he meet the quota of sparkling, hairlessness, beauty, deep voice, and vanity, he's also a muscular, oversizedbodybuilder, who constantly flexes and lacks an indoor voice.
At the end of the manga and second anime, Alphonse is revealed to be a gorgeous bishonen.
He's arguably even more of one in the movie of the first anime, since he shares his brother's long hair.
Joshua Christopher is the most obvious example from the series—he's quite thin (even implied to look underweight at one point), has pale blond hair and blue eyes, and looks quite a bit like his sister.
Aion is a bit more borderline—he's actually quite muscular when he takes off his Badass Long Coat, but his long, white hair does a lot to give him an edge of androgynous beauty. He's maybe a bit more of a biseinen.
Chrono is a tricky one. In his true form, he's a bit rough around the edges and his outfit goes out of the way to highlight his muscular chest, but in his Sleep Mode Size, he's got longer hair and looks much younger (and thus cuter). However, he still has moments of looking quite pretty in his true form, and a flashback in the manga shows him with long hair, which definitely qualifies him.
Ayasegawa Yumichika is defined by his connection with beauty. Not only in looks but in lifestyle, too. He even accepted a lower rank in his squad than he had to because he thought that, in kanji, the number 5 was more "beautiful" than 4.
Byakuya Kuchiki is very bishonen and is often voted "Seireitei's Sexiest Male Shinigami" by the Shinigami Women's Institute.
Ishida Uryuu has a very slender, delicate build and an exceptionally fair complexion for a male character. He takes after his father Ryuuken, who is a Silver Fox, and who was his school's heartthrob when he was Uryuu's age.
Itsuki Koizumi in Haruhi Suzumiya. That is, in a Brigade of crazy people, with a cynical Deadpan Snarker who constantly tells him that no one cares about him. He probably just appears to be one, but he sure seems to make most women blush. As Kyon puts it, 'A face I wouldn't introduce to my girlfriend'.
Il Palazzo of Excel♥Saga is very pretty and has long, silver hair.
In just about every Shojo manga and whatnot, Bishies are everywhere, or, at the very least, there is guaranteed to be at least one bishie main character since the male lead is 99.9% assured to be one.
Hakuoh of Duel Masters has to be one of the bishiest, with his slender build and long, flowing, silvery-blue hair.
Ayato Kamina from RahXephon is pretty enough that he'd probably not look out of place in a dress. There's also Dr. Itsuki (who bears a suspicious resemblance to the above-mentioned Rossiu) and Souichi Yagumo (who bears a suspicious resemblance to his own girlfriend, Kim).
The four older knights in Pretear are examples of this trope, particularly Kei. Goh is borderline, but he makes up for it by baring his midriff in his knight outfit.
Mytho in Princess Tutu has eyelashes thicker than his girlfriend's. Femio is also an over-the-top parody of this type. Ironic in that Vic Mignogna plays an only slightly toned-down version of Femio in Ouran High. Even better there because, no matter how cheesy he is, the girls there actually fall for it.
Several characters in Yu-Gi-Oh!, including at least Yami Yugi, Seto Kaiba, Malik Ishtar (and how!), Ryou Bakura, Yami Bakura, Pegasus, Ryuji Otogi, and a number of minor supporting characters.
Mahou Sensei Negima! gives Negi some magic age-up pills, turning him into one of these. He's also a dead ringer for his father, who was also a bishonen. Albireo Imma probably counts too. Teenage Kotaro definitely counts as well.
Even Claymore manages to have one of these in the cast: Isley of the North.
Many of the characters from Rurouni Kenshin, especially the titular character, Mr. Pretty Boy Swordsman himself. Depending on the quality of the animation in an episode of the anime, particularly in the later episodes of the series, and you know, just about all the time in the manga, Kenshin is very pretty despite the fact that he's a terrifyingly powerful swordsman who even the manliest of men are afraid of. It doesn't help that, towards the end of the manga and in most of the official artwork, his hair always looks extremely long and flows like a bunch of ribbons. Just look at these pictures: , , , . I rest my case. And even more so in the Trust & Betrayal and Reflections OVAS.  And then, you know, there's Soujiro, Aoshi, Sanosuke, and, heck, even Hiko qualifies, although he's pretty manly. Observe: .
A good amount of the male characters from Black Butler. Except for Baron Kelvin, who realizes this and is obsessed with "becoming beautiful", Georg von Siemens, Jumbo, Lord Arthur Randall, Azzurro Vanel, Fred Aberline, Damian, and Doctor.
Kantarou Ichinomiya from Tactics is a white/very light brown? haired bishie, who is annoying and greedy, but overall a good person. He is so young looking, nobody really knows his age. It is implied that he is much older than he appears. Many other guys in it also qualify.
Sanji recently has been beating people pretty. His first victim, a hideous Wanze, was rapidly kicked across the face until he became (to his horror) this trope. Later, Sanji, fighting his bounty poster look-alike, does this again, much to his foe's joy.
Played for Laughs in Boa Hancock's romantic fantasies about the normal looking main character Luffy - she sees him as typical Bishonen with a full Bishie Sparkle and brown eyes, as well as speaking with a more mature voice than he actually speaks with.
The series now has its first definitive Bishonen. His name is Cavendish. Not only does he have the Bishie Sparkle, he also has large, glinting eyes, a trait commonly used only for female characters. His glinting eyes pretty much drive the point home, because the eyes of male characters in this series rarely glint, if at all.
Almost every male character in Saiyuki. The four main characters are these, of course, but also Kougaiji, Dokugakuji, Hazel, Koumyu, and Ni Jian-Yi/Ukoku.
Depending on who you ask, a good number of the male cast in Naruto could qualify as Bishonen. Notable examples include Haku (to Dude Looks Like a Lady levels), Benten (Filler Villain to Dude Looks Like a Lady levels), Sasuke, Itachi, Kakashi, Deidara, Sasori, Neji, Suigetsu, Kimimaro, (arguably) Orochimaru, Kabuto, Sai, Gaara, Shikamaru, Kiba, Utakata, and the titular character himself. Naruto definitely counts, considering that he has his mom's AND his his dad's looks, though this trope is mostly appropriate only after the time skip. Also, the Fourth Hokage, aka Naruto's dad.
Many characters of MÄR, on both sides of the good/evil divide. Alvis◊ and Nanashi◊ are this, combined with the headband of eyecovering. Every once-in-a-while, they even comment on it in-universe.
In AKIRA, there's Kai, aka Kaisuke, who's short, slim, well-dressed, girlishly faced, and can knock a guy through a window. Being relatively sensitive and apparently crushing on Kaneda in the manga and Yamagata in the anime, he's often perceived as a young homosexual.
The titular Yakumo from Psychic Detective Yakumo fits this trope to a T. Haruka even thinks he's a "beautiful person" when she first meets him. Also, a good amount of male college students who pop up.
Special A: you'd think a beauty contest was part of the Special A qualifying exam, looking at the male cast. The girls, too, unsurprisingly, since a beauty exam is almost mandatory to be part of most Shoujo casts.
There is a lot of focus on people's looks in Jyu Oh Sei, despite the action being set mostly on a jungle planet with vicious plants and a murderous climate that's used as a prison for criminals. All of the male characters are◊ exceptionally◊ pretty◊.
Miki Kaoru from Revolutionary Girl Utena is mentioned to be one by Utena in the preview of the episode of his first appeareance. Also, practically every guy in the cast.
Aburatsubo from Magic Users Club. He's tall, has long red hair, and is gorgeous...with the requisite legion of fan-girls expected for any bishonen. The only problem for said fangirls is that he's gay and in love with the main character, Takeo.
Star Driver's Takuto Tsunashi. "Galactic Bishonen" isn't a nickname; it's his official title as the Chosen One
Most of the rest of the male cast count as well. Especially Sugata.
Most other young-ish male characters also count, like Oz, Elliot and Leo. And the latter even more so after an Important Haircut.
A notable example is Liam; the fact that no male or female pronouns were ever used to refer to him for some time didn't help. They fixed this in the anime, however, giving him less feminine features and a decidedly male voice.
Kusuriuri/the Medicine Seller from Mononoke. Even his manner of dress combines gender conventions, and characters in the series make note of how attractive he is.
Most of the males in Shugo Chara! are known for their Bishieness.
Nagihiko Fujisaki takes the Bishie Ribbon in the world of Shugo Chara. When Hinamori first meets Nagihiko, he is actually posing as his female alter ego, Nadeshiko. Why is this boy posing as a girl? The Fujisaki family tradition is for the males to pose as females to learn the ways of Japanese Dancing.
During the series, Nadeshiko tells Amu that 'she' and Nagihiko are twins (the rest of the Guardians know about Nagi & Nade, but Amu Hinamori doesn't). It's not until late in the series that Nagi reveals the truth to Amu.
Akiyoshi of Kawaii Akuma (and its sequels) is often told that he is "cute" or "pretty", and this caused him to develop an inferiority complex. Naruse is also incredibly Bishōnen, to the point of being a Dude Looks Like a Lady.
Death the Kid, Gopher, and Kishin Asura from Soul Eater.
Many characters in Axis Powers Hetalia are actually mislabeled as this (and the fanart doesn't help); the art style is very Puni Plush, thus the majority of the male designs are simply moe. The ones that aren't moe usually fall more into the hunk category (and even then, there's overlap) and there's even a few bara-type characters, such as Turkey. The purest bishounen in the series would be Austria.
Lets not forget the most extreme cases, Kakyou (who, as if it was possible, is even more of a Bishonen here than in X, and Ashura-Ou, who quite a few fans are still convinced is a a woman (though Ashura was technically genderless in RG Veda and actually has no specified gender in this work).