The Doctor: Inferior?
EMH 2: Beady eyes, terrible bedside manner. I recognize you.
Bob is an Unlucky Everydude, the classic underdog. He's a terrible student and a klutz on the field. He can't be an underdog if he's attractive to other people, so Alice will occasionally comment that he's not much to look at. You don't see what's so ugly about him, but it's an Informed Deformity and maybe he's Hollywood Homely. Then at some point in the story he meets Charlie, the in-universe stud of the show whose beauty is admired by all (especially Alice). There's one problem, though. He really isn't any more attractive than Bob. That's odd...
Due to Generic Cuteness, Only Six Faces and possibly Beauty Equals Goodness, it can be very difficult to differentiate an average or even ugly looking character from a beauty, with the only truly unattractive characters being Gonks. This can make it especially odd when the supposedly average-looking main character meets the in-verse Bishōnen of the show, and you realize the only real difference between them is the hair cut and maybe some Bishie Sparkles.
So how do you tell the audience the character is supposed to be average or unattractive while still making them easy on the eyes? Make their eyes beady. It's not that beady eyes are really all that ugly (just goofy looking), but in a world where beautiful doe eyes are the norm, it sort of makes sense that this character would be considered unattractive in comparison, even if they otherwise look like everyone else.
To summarize, these eyes are a visual cue that the character is a loser or outcast, and obviously they'd be considered unattractive by their peers. If this character is a main character or even given some time in the spotlight, their eyes will be less beady during serious moments or if they show personal growth.
Compare and contrast Face of a Thug, since they too have beady eyes, though those elicit a different reaction.
- Simon of Tengen Toppa Gurren Lagann was considered gross and weird by the girls of his village, though that's probably more to do with the amount of time he spends digging and generally not paid much attento to by the adults. The Black Siblings also considered him completely unremarkable, especially in comparison with Kamina, his big brother figure and hero (who, to be fair, was a Hot-Blooded Walking Shirtless Scene). Pretty much the amount of people who did not have this view of him at any point is few and far between. The only one who beleived in him from the start was Kamina (and later Nia when she met Simon.) His eyes becomes less beady throughout the story as a sign of his Character Development. He learns to be himself and believe in himself, becoming a strong and wise hero. By the end, his eyes' resemble Kamina's and he has long surpassed his soul brother.
- Sena from Eyeshield 21 spent his entire life being pushed around by bullies, and started the story with very beady eyes (practically dots). By the end of the series, Sena's eyes are more normal looking.
- Tsuna of Katekyō Hitman Reborn! starts the series as a stereotypical loser complete with the beady eyes to match. As the story progresses, he not only experiences personal growth (and many power upgrades), but somehow goes from beady-eyed to moe-moe. Though that's probably more to do with art evolution, as everyone in the story gets more and more pretty.
- Shikamaru of Naruto graduated second worst of his year, and is assumed to be a lazy loser till people discover he's got an IQ of 200.
- Ataru of Urusei Yatsura is one of the unluckiest and perverted characters in the Rumiko Takahashi universe. He's also the most beady-eyed.
- Kai Shiden of Mobile Suit Gundam is a Lovable Coward who chases skirt and snarks on the relatively inexperienced commander Bright Noah. In a subversion of the usual formula, he retains his beady eyes even when he develops into a combination Adventurer Archaeologist-Intrepid Reporter in Zeta Gundam.
- Hideki from Chobits, big time. He's a broke, spastic, computer-illiterate ronin who couldn't talk to a girl or get into college to save his life.
- Yuuji from Tona-Gura!. It's parodied in that when he tries to look chivalrous, his eyes adapt the "regular anime" style.
- Masao from Shiki is sort of an unusual case, in that he lives in a Cast of Snowflakes and is honestly meant to be ugly, tending toward Ugly Cute at best.
- The Producer from The iDOLM@STER 2: The World Is All One!! begins as just another loser office worker and, in a cast full of young star eyed pop idols, is the only one with beady eyes. Later on, a pair of glasses given to him by his idol wards attempt to rectify this, paralleling his clean break with his old life.
- Aitsu no Daihonmei's Yoshida is a simian, pint-sized idiot with a disfiguring scar, whom his female classmates frequently beat up for inexplicably monopolising the attention of the most popular boy in school, Satou, a typical doe-eyed Bishōnen.
- This is the case for Haru in the anime taken from My Little Monster. The use is inconsistent, as once he starts smiling at all the girls they start to really like him, even though he remains drawn beady-eyed. Also, the beady-eyed-ness is in-universe, as Mi-chan constantly wears sunglasses to prevent his beady eyes from scaring away his clientale.
- Shouya from A Silent Voice is a protagonist example. He used to be a bully as a kid, which caused him to be ostrasized and used a scapegoat. He has small eyes compared to most other character's huge anime eyes.
- Haruyuki Aries, protagonist of Accel World, has beady little eyes, especially compared to the more defined eyes of everyone else in his world. Not surprising considering he's "a boy at the bottom of the school social order." Interestingly enough, a fan theory speculates that he's actually broadcasting this image of himself via the augmented reality capabilities of his neurolinker.
- Hikigaya Hachiman, the protagonist of My Teen Romantic Comedy SNAFU, is often told by other characters that his eyes resemble those of a dead fish, symbolic of his bleak outlook on life.
- Buffy the Vampire Slayer. In the Musical Episode song "I'll Never Tell", Xander's "beady eyes" are among the list of complaints which Anya has about her fiance. Xander certainly did fit the Beady-Eyed Loser trope for the first few years of the series, though by this time he's actually quite successful, running his own construction business.