Arashi no Yoru ni: Mei the goat. He is a sweet little goat who's just so darn dorky and clumsy that he steals the spotlight from Gabu most of the time.
This is the core of most of the Asteroid in Love's character designs—one part cuteness (in the moe sense), one part nerdy obsession. Astronomy for Mira, Ao and Mari, geology for Mikage and Chikage, cartography for Mai, and meteorology for Yuu.
Finland, who is not only a sweet-tempered, friendly and talkative Nice Guy, but has a pretty strange naming sensenote One of the names he thought up for his and Sweden's pet dog was "Bomb Bastard" and is irrepressibly enthusiastic about sweets and saunas.
Osaka pretty much has her own cult following due to the trope. She's a spacey Cloudcuckoolander, who believes Chiyo's father is a weird orange cat thing and once thought Chiyo's pigtails were detachable, but that's part of what makes her so adorable.
Sakaki seems like a cool and aloof girl at first glance, but she's really a kind, shy and introverted girl who adores cute things, like cats or Chiyo. She tends to quietly Squee! at the sight of them, and like Osaka, tends to daydream and think Chiyo's dad is a cat.
Rukia has had her moments: her love for cute things and bunnies-specifically chappy, not to mention her drawing skills (or lack there of), plus her "innocent (and dramatic) girly schoolgirl" act she puts on in front of Ichigo's family and classmates is too adorable.
Rin Okumura. He's Book Dumb, somewhat kluzy at times, goes all awkward when it comes to girls he likes, is very childish - especially with friends - and is an AMAZING cook. This◊ popular image says it all.
Yukio Okumura. Generally the calm, collected guy...but put him in a social situation and he generally falls to pieces as his basic shynature comes to the front. Multiply this if it involves Shiemi.
Konekomaru is shy, shortglasses-wearing smart guy who adores cats.
Shiemi Moriyama is downright adorable, so darned sweet, as well as terribly awkward around people.
Bokura no Kiseki: Gerald Frolio. He's an awkward and sort of nerdy priest, who clearly has something of a crush of his country's Princess Veronica. This applies to his reincarnation from the series' present timeline, Midou, to a certain extent as well.
Bunny Drop: Pointed out when Daikichi notes how unfair it is that "Michan" (the dad of one of Rin's classmates) is also extremely clumsy. It was like he was scientifically designed to be as attractive as possible, and the clumsiness just makes him more adorable.
Kosuke, Daisuke's dad. He's very clumsy and kind-hearted.
Darker Than Black: This is about half the point of "Li Sheng Shun". He's so adorably inept, clumsy, kindhearted, and naive that you just want to hug him, and nobody would ever suspect he's secretly the Black Reaper, the most badass and stoic guy in a series full of emotionless killing machines.
Conan himself. In the beginning of the series the only clothes he's seen wearing are his miniature suit, complete with a bow tie. This combined with his cute ways of expressing his feelings and his Sherlock Holmes obsession create top quality Adorkable material. He can also be classified as an out-and-out mystery geek, not just a Holmes geek.
Conan's dad, Yusaku Kudo. He's a mystery writer who gets a bit too excited about mysteries. Also, his glasses rock. And his wife/Conan's mom Yukiko mixes this with One of the Kids, Tsundere, and being really damn pretty.
Joe Kido tries so hard to be the responsible Team Dad of the group, but is also a totally neurotic nerd. He starts to grow out of the neurotic nerd part of his personality later on, but no matter what his adorkableness remains.
Davis/Daisuke who is such a ditzy goofball and can be rather silly around his crush. One of the dorkiest things to behold, yet cute.
Ken displays traits of this once he joins the team as a contrast to his former Kaiser persona; he's incredibly awkward and somewhat socially inept, but it only makes him come off as more of a nice guy.
Wormmon's childlike behavior and voice make him incredibly cute and endearing.
Digimon Tamers: Takato. The kid's just so earnest, it's hard for him to be anything but. It's really easy to see in his interactions with Ruki, who can go Tsun-Tsun when she realized he's added too-girly emoticons to the e-mail he wrote in her stead, and dere-dere when she pretends to be more annoyed then she is at his failed attempt to keep her surprise birthday party a surprise.
Arale, a clumsy and curious Robot Girl who is clueless about how the world works. The small, cute-like appearance, huge glasses, along with her perpetually bubbly and innocent personality make her very endearing.
Obotchaman, Arale's love interest (originally created to be her Evil Knockoff) also qualifies. Unlike Arale, he's extremely well-mannered and polite. He's also shy, romantic and so smitten with Arale that he gets adorably awkward when talking to or about her.
Son Gohan, especially as a teenager. He's such a sweet, friendly, good-natured guy, yet also very studious, and he gets into many embarrassing social situations, and he has questionable taste in fashion and, er, superhero poses.
Yamcha was adorkable during his teenage years but he grew out of it a little as he got older. Yamcha was afraid of girls and super awkward around them when he was a teenager, even though his dream was to fall in love and get married. He even wanted to use the Dragon Balls to make it so he would not have panic attacks around girls anymore.
Kid/Teen Chi-Chi (the former moreso), because of her massive crush on Goku and her constant blushing and crying. You can't help finding her Adorkable.
Goten. Gohan's friendly, good-natured hyperactive brother. His innocence and childish personality is what makes him adorkable.
Goku. Huge goofball with a high voice. Having to grow up by himself, isolated from a lot of the world, he was very childish and adorably curious and oblivious to a lot of things as a child, such as love, or even what girls were like. And even though he wisened up as an adult, he still retained a lot of his adorably goofiness and childishness.
Future Trunks. He's a polite, friendly and somewhat shy young man despite having spent practically his entire life in an apocalypse. Due to being in unfamiliar territory, he's prone to being easily flustered, but he doesn't hesitate to praise his friends.
Celty every time she tries to do regular human things like cooking or playing video games or when she gets scared of aliens and cops
When not in rage mode Shizuo's a friendly and insecure guy. Too bad it doesn't happen that often.
Free!: Rei is book smart and serious, but still does ridiculous things as if they were normal, like trying on silly patterned swimsuits with gusto, calling Rin "Rin-chan-san" note since Nagisa calls him "Rin-chan", and pretending to be a detective and making sound effects while spying on Rin.
Fruits Basket: Kyo Sohma tries to act all macho, but in reality he's really a lovable dork, especially around Tohru, his love interest. He's also the family punching bag.
Full Metal Panic!: The normally calm and Stoic Sousuke Sagara becomes a complete dork around women or when confronted with romance or anything sexual. Both Kaname and Tessa admit that one of the reasons they like him is that even the PTSD-riddled, terrifying military persona can't mask the fact that he's ultimately an earnest, socially awkward dork just trying his best to be helpful (even if he's terrible at it.)
A large part of the manga's humor stems from Leo, a hardened badass knight, becoming flustred and awkward whenever confronted with Houli's feelings for her, or hers for him. She also gets very eager when shopping in a weapons shop, speaking of the deadly implements with such innocent joy that Houli has to Lampshade it.
Helga takes this to extremes, as her complete lack of social skills and her desire to be friends with Leo make her come off as incredibly adorable, even with her Face of a Thug.
Jagaaaaaan: Once her feelings for Jagasaki become apparent, Bell begins sporting an almost permanent Luminescent Blush around him and she ends up being hilariously adorable whenever she confesses her feelings for him in her usual blunt ways.
Yasuho Hirose has a number of moments that shows she's just as goofy as Josuke, such as her realization that she can lick her own elbow.
Kare Kano: Yukino Miyazawa is a gifted high school student lauded by classmates and teachers. This apparent brilliance, however, is mainly used as a means to garner praise. At home, Yukino is very dorky.
Log Horizon: Akatsuki roleplays being a ninja constantly, has trouble conversing with other people, but is very earnest, so when she speaks, what comes out is sometimes very awkward.
Monochrome Factor: Kengo has this in spades. Not only is he a sweet lovable idiot who bounces back nearly all the time even though he keeps getting treated as the punching bag of the group, he looks the cutest when he's crying or smiling (which is nearly all the time). too bad he gets killed off gruesomely. even worse, he went out with a smile, accepting his own death for the sake of his friends.
Ochaco Uraraka herself is adorkable whenever her crush on Izuku is brought up. One anime-exclusive scene has her very physically close to her friend when excitedly bringing up the training camp, and gets confused when she notices him turning beet red. When she notices how physically close she was, she gets an adorable Luminescent Blush of her own and distracts herself, and a couple of her classmates, with a song and dance number.
Even All Might, despite being the Symbol of Peace and an imposing man, manages to be adorkable at times thanks to the sheer enthusiasm he has about being a hero. He once made a bombastic entrance that his protégé Midoriya was in the vicinity, right before offering to eat lunch with him; even Uraraka lampshaded how adorable that was.
Tenya Iida is a very earnest young man, so dedicated to being a hero that he gives 100% of his determination into everything he's tasked with, even playing a villain or simply dancing on stage.
Momo Yaoyorozu can be a bit too enthusiastic about a lot of stuff when she was taught to be a proper lady. She claims she has serious reasons for acting the way she does, but everyone else can see that she's got the heart of a curious and eager little girl wanting to act like a normal girl would.
Kyoka Jiro is normally very forward, but bring up the subject of her personal and innermost desires, usually music, and her adorable shy streak emerges. She even engages in Shy Finger-Twiddling with her earlobes when flustered.
Fumikage Tokoyami has a tendency to say dramatic things about situations that don't quite deserve them, such as calling a recreational game on their school trip a "mad banquet of darkness", or giving his attacks overly dramatic and dark-sounding names. Even his room's decor is dark and spooky, and he got angry when no one took it seriously.
Koji Koda becomes this later on, in no small part due to his shyness and love for animals which caused him to bring a pet bunny to his dorm room.
Inko Midoriya, Izuku's mother, is just as adorkable as her son. She's timid, easily startled and prone to overreacting, but also a doting mother who is constantly worrying about the safety of her son, panicking to the point that she can barely get across the floor on all fours, pacing back in forth in the hallways, and crying so much that she knocks herself unconscious from dehydration.
Jean from Nadia: The Secret of Blue Water. Not only is he intelligent, he is also generous, sweet-natured, caring, friendly, loyal, naive, and dedicated to what he likes. He's quite brave, as well. Of course he's naturally green when it comes to social graces around the opposite sex, but in a way it proves to be an asset. Nadia's English voice actress once said that she would date someone like him "in a heartbeat".
No one could have predicted that Hashirama, the First Hokage, was this. He noticeably stands out against his brother, the Second Hokage who is very stoic while the former is goofy, friendly and just plain Keet, cheerfully admitting he spoiled his granddaughter rotten. One person even commented how it was hard to believe that such a cheerful, happy-go-lucky person used to be one of the strongest shinobi in the world. Proves to be a Crouching Moron, Hidden Badassby intimidating his brother, Sasuke, Juugo, Suigetsu, and Orochimaru through sheer willpower without moving an inch.
Mari Makinami from Rebuild of Evangelion can't see without her glasses and, outside of her EVA, is socially awkward to the point that Rei could fit in better than her.
Shinji Ikari, who apologises a lot, plays the cello, is mostly polite to everyone, and is self-deprecating (but without the humourous irony). It's probably why he appears to have UST with many of the female characters in the cast.
Rei, who is shut off from practically everyone to the point of not knowing appropriate responses to others. For example, Shinji suggests that she should try smiling and Rei takes inspiration of how to smile with a memory of Gendo smiling at her.
Asuka occasionally can be this, particularly when she's being verytheatrical or showing off to strangers. When she's not coming off as an Alpha Bitch, it can be amusingly-endearing.
Outside of the Straw Hats, Boa Hancock of the Seven Warlords of the Sea is this, but only around Luffy. Hancock is usually too serious to be adorkable, but she acts like a Smitten Teenage Girl around Luffy, has frequent Imagine Spots about him, and tends to misinterpret a lot of what he says for proposals or declarations of love.
Tashigi has shades of the trope, being competent in battle but a Cute Clumsy Girl with a great love for swords outside of battle. She's also prone to mistaking random people for her superior officer Smoker without her glasses.
For a spoilerrific example, we have Charlotte Pudding, who is a double subversion of the trope. When the Straw Hats first meet her, Pudding is very kind, ditzy and dreamy, seeing Sanji as her prince charming. Then, her true colors as a cruel and sadistic person get revealed, and her adorkable aspects get chucked out of the window. However, when she pulls a HeelFace Turn, she becomes adorkable again, being constantly flustered around Sanji to the point of acting like a Tsundere.
Shirahoshi is an adorable young princess who, due to having been sheltered in her room for a good portion of her life, has a giddy and reaction nature to seeing new sights that is really too cute for words.
Coby is a shy and timid boy, and even after taking several levels in badass, remains as flustered as ever when his heroic deeds are brought up.
Fearsome and violent though he may have been introduced as, Bartolomeo is a huge fanboy of the Straw Hats, and gushes around them every chance he gets.
Ouran High School Host Club: Tamaki. He has the handsome bishie looks and is very adept at flirting with girls he doesn't much know, but around friends (not to mention his actual love interest) he becomes a lot more of a lovable idiot.
Maybe you're just innocent, unyieldingly innocent...
Pokémon: Ash Ketchum, at least in the older seasons. He was rather klutzy and somewhat dim-witted, but also a really sweet kid with an enormous heart, and already a pint-sized Bishōnen to begin with. The Sun and Moon series brings this trope back in full throttle, while keeping his developed insight and prowess since then to make him an adorable Dork Knight.
Team Rocket's Jessie, James, and Meowth. Jessie for being a vain but lovable diva, James for just being so precocious and Meowth cause he's a frickin' talking cat with a New York accent! They serve as the villains but are just so gimmicky and so... fail that they aren't even threatening anymore. Their determination is admirable too.
May for being brave, optimistic, kind, and sometimes awkward.
Dawn's Buneary sometimes shows shades of this when around Pikachu by blushing and hiding her face in her fur.
At times, Cilan's hammy behavior makes him come off as this.
Does Serena fit this trope? Let's see: Acts like a schoolgirl around her crush, fumbles around her words when people ask if her and said crush are a couple, always comes off as sweet and endearing in everything she does...yep, she definitely qualifies.
Clemont's poor physical condition and obsession with technology, just to name a few of his endearing quirks.
Lillie is an Adorably Precocious Child, being highly educated in Pokemon, unfortunately she spent most of her early run with a phobia of touching them, and even when it's conquered, she remains an jittery Ditzy Genius while still huggably sweet and polite.
Lucy in "Battle Frontier" has these moments when she blushes over Brock's infatuation with her (she returns his affections).
Read or Die: Yomiko Readman. The quintessential bookworm. So nerdy. So cute. And so very, very scary.
Robotech: Max Sterling. Long hair, glasses, an always-friendly disposition, and his excellence with video games helping him also become The Ace fighter pilot (it's unclear whether being an Ace made him good at Veritech games or vice versa, however). That he's also voiced by master-Adorkable voice actor Cam Clarke helps. His original Super Dimension Fortress Macross counterpart Max Jenius has plenty of this too.
Ami Mizuno/Sailor Mercury, a Cute Bookworm and a Shrinking Violet who tends to have a difficult time making new friends (despite being humble and gentle), is Allergic to Love, frequently blushes whenever Usagi is nice to her and often embarrasses herself whenever she thinks out loud (usually about romance or something X-rated).
Mamoru is somewhat of a Bumbling Dad forced to deal with the antics of Usagi and the Kid from the Future, who are both fighting for his attention, but he also walked in front of traffic and fell over and supposedly went to a bar with Artemis — a cat. As Tuxedo Mask, his speeches are off-the-wall and hammy, he's melodramatic, and he has created his own merchandise (a puppet, slippers, etc.)
Outside of her Sailor Mars persona, Rei became this in the 90s anime, talking in the Third-Person Person, the frequent Gilligan Cuts of her claiming that she's the most graceful of her friends, to her falling over and embarrassing herself, and the petty squabbles that she and Usagi frequently have. In one episode, she attempts flirting with The Starlights band by talking like an ojou but it scares them off.
Minako Aino/Sailor Venus at times. Like Usagi she's a bit of a ditz (also a Malaproper in the original anime), and an overall perky yet lovable, cheerful and fun-loving girl who laughs at her own corny jokes even when everyone in the room is groaning.
Umino is a classic nerd with tousled hair and weird-looking glasses that engulf his face, who has a notebook full of gossip about new students. Then there's the moments that he and Naru are Sickeningly Sweethearts who are devoted to each other.
Became an Establishing Character Moment for Haruka/Sailor Uranus, a hard-nosed Aloof Ally of Sailor Moon who uses brute force, when in the SuperS movie, her girlfriend Michiru/Sailor Neptune casually makes a double entendre which makes her blush. Up until this point, Haruka had been a known Handsome Lech who found amusement in flirting with many women, but it turns out that she cannot take flirting back, especially from her girlfriend. It must have made an impact because later appearances showed Michiru frequently flustering her with snarks, and then there's the adorkable moments when she and Usagi interract, which is reminiscent of a big brother trying to deal/protect his wacky, trantrum-throwing little sister.
Kaori Senoo from Tsuruga, a timid and socially awkward girl, who also doesn't know much about mahjong (for example, calling out riichi without getting the stick, and not realizing when she has a Yakuman hand). Her character selection screen in the PSP game lampshades this trope.
"Somehow the sight of this timid second-year student fidgeting away is just too captivating."
Yoh Asakura, a ditzy, laid-back protagonist who is also adorable.
Manta could probably surpass Yoh in this department, since he's a chibiSmart Guy. In fact, he's probably the anime character personification of the trope.
Despite the Values Dissonance taking place, Chocolove could qualify. His persistence on making people laugh is awfully endearing, and in a way, he's sort of an Ugly Cute.
The title character from Skull-face Bookseller Honda-san. Aside from being earnest, knowledgeable, and hardworking, his interactions with customers are pure gold. Just look at his awkward reaction to the handsome old man. When he's approached by a group of girls asking about what he thinks the hottest BL is, his lower jaw falls off.
Slayers: Gourry Gabriev is often viewed as adorkable by fangirls. He's a badass swordsman, but his terrible memory (at least in the anime) and tendency to be really sweet and a genuinely nice guy make him totally Adorkable. Less so in the original novels; Gourry's actually got a bit of a dry, snarky sense of humor and he's more observant than Lina gives him credit for. Gourry's anime portrayal seems to be a Flanderization of how Lina perceives him; viz. as nonmagical as it's possible to get and therefore a complete moron.
The titular protagonist is this so much. Being a literal Fish out of Water, she doesn't know a whole lot about the surface, and has a child-like naiveté and curiosity for a lot of mundane things of normal human life. Mix that with some genuine naiveté and some Genki Girl tendencies, and you get a very adorkable girl.
Keiko Furukawa is a cute young policewoman, and always eager to help and protect whoever she can. Unfortunately for her, she's a Cute Clumsy Girl with No Sense of Direction, and tends to be forgetful and incompetent. Bless her heart though, she really tries to do a good job.
Being a shut-in gamer for most of his life, Kirito is not very good with social interactions, especially when it comes to girls, having a tendency to trip over his own words so others gets the wrong idea.
Taiga Yagura. Aside from his rather poor social skills and his love for bizarre-flavored ice creams, he's the kid who proudly declares that a blobby stick-figure he crafted out of wood is Backdraft.
Sasagawa as well. She's a sweet, gushing robot fangirl. Normally she tries to stay professional, but occasionally will slip and start obsessing while on TV (her career being a news announcer).
Somehow, even Karigari manages to have an Adorkable side. Normally an Insufferable Genius, who always loves an opportunity to boast about his knowledge on science, history or anything else, he's so awkward around his crush, Sasagawa, that he can barely speak with her.
Even Kurumada, when he geeks out over his own machines and acts so overprotective of them.
Trigun: Vash fits this quite well, easily falling into being a Badass Adorkable during times of comedic calamity that tend to follow him.
Uchi no Musuko wa Tabun Gay: Hiroki is a young, easily excited and sweet boy that gets easily flustered and is very obviously in love with one of his classmates. It's shown that a number of people In-Universe think he is cute too, including his mom, his brother, his brother's friends, and even his crush.
Waiting in the Summer: Kaito wears glasses, frequently dorks out with his old-fashioned camera, always nice but very awkward...we have a winner!
Yo Kai Watch: Komasan is an adorable,shy, and sensitive Yo-Kai that travels and currently lives in a city with his little brother Komajiro. Throughout the anime, Komasan is hired for various stuff like a janitor and a detective. Then there is Komasan and Komajiro's human forms that are just as cute as their Yo-kai forms.
Yugi Mutou, the actual one, not the Super-Powered Evil Side. He's a slightly dopey, socially awkward kid whose deepest wish in the first chapter is just to have a few friends. He gets them though, because people finally start seeing and appreciating his Incorruptible Pure Pureness.
Ryo Bakura also qualifies, if he isn't more so. He's the shy kid in the sweater who's obsessed with games of all kinds and has very little friends. Too bad he was downplayed in the anime. And again, this is the REAL Bakura we're talking about. The Spirit inside him is... less adorkable.
Team Taiyou, also from 5D's. Most of the WRGP finalists are elite duelists with expert decks and strategies, and have the attitude to go with them. Taiyou, on the other hand, are just a couple of poor, friendly guys from the country who eagerly want to prove their worth to the world. The hijinks that ensue when they try to put together a bike and deck are hilariously endearing.
The best example from Yu Gi Oh Zexal is III/Trey, a Rose-Haired Sweetie who loves ancient artifacts and civilizations. When he sees everything Yuma got from his father's adventures stashed in his room, he quickly starts geeking out over everything there. It means all the more to him considering his deck is based around such things.
×××HOLiC: Watanuki, at least before Yuko's death. The way he expresses himself tend to be overly exaggerated as well as hilarious, making him even funnier as well as cute. The adorkableness adds even more with Todd Haberkorn playing him in the English dub.
Shin-ah in Yona of the Dawn is not used to being around people due to his isolated childhood but earnestly tries his best for his friends who find him endearing, although sometimes confusing.