Bachou Mouki from Ikkitousen is deathly afraid of snakes.
Motoko Aoyama from Love Hina is afraid of turtles. So her fellow tenants adopt one that can fly.
Ymir from Queen's Blade can't stand snakes. When she met Echidna, she spent the following night sitting up, axe in hand, convinced the snakes would come when she slept.
Yura of the miniseries Wasted Minds is afraid of snakes. At one point, when she sees something she thinks is a boa constrictor, she's too scared to help her partner, Tamuro, out of its grasp. After she discovers that "the snake" is actually the trunk of an aggressive elephant, she fearlessly flips it over and slams it into the ground.
Yura: Boa constrictor!
Tamuro:There aren't any boa constrictors in Japan! Help me!
Yura: I hate snakes!
In the manga version of Ace Attorney, Jirou Kimura was scared to death of spiders. He went apeshit and committed suicide after his boss Komori Akamune, who couldn't stand his arrogance, locked him for hours in a room full of them.
Sakaki is also revealed to be scared of horseflies, among other things (See the "Various" category below).
A plot point in a Detective Conan case. Rich Bitch Hiromi Yamazaki is completely terrified of bees due to being allergic to their sting (and she almost died when stung by one as a little girl)... and the person who killed her is Genre Savvy enough to actually use bees as one of their "killer weapons". More exactly, they caused her to panic at the sight of some bees released in the highest floor of her Big Fancy House, then covered the door handle in honey so there would be more bees there, and when Hiromi leaned on a wooden rail... the rail was "broken", causing her to fall to her death.
Franken Fran: Adorea is scared of cockroaches, and had quite the reaction when she and Okita happened to walk into a room that was full of them. From the same chapter, a young woman who is obsessed with cleanliness freaks out when a cockroach falls into her tea.
Tokine, in Kekkaishi, she is the more experienced, much smarter of the two kekkaishi, tough as nails and able to handle anything....except cockroaches. She definitely hates those cockroaches.
Mikan from Rising X Rydeen is a tough girl who can move as fast as lightning and fire powerful lightning blasts but she is deathly afraid of cockroaches.
Nano in Nichijou is scared to death of cockroaches. In one sketch she has one trapped under a bowl and would rather tape the bowl to the table and throw the table itself out than risk it getting free. She also faints at the sight of a mosquito (which she herself killed).
Perona from One Piece is absolutely terrified of cockroaches. It only took Usopp a bunch of fake ones to make her flip her shit.
It's not really surprising that Oda made Nami afraid of bugs as well, but Sanji? He's just as terrified. It's even more hilarious, when Usopp is the only one of three who is not afraid of insects and finds them cute.
Misty of Pokémon has three things that she hates most of all and bugs are one of them, as exhibited when Ash catches a Caterpie in one of the first episodes of the show and Misty cannot stand being near it (though she's less repulsed by the prettier bugs like Butterfree and Ledian). This is exhibited many times in the show, like during the episode with the Bug Catching Contest where she freaks out whenever a wild Bug Pokemon even comes close to her. Encounters with Ghost Pokemon also give her nightmares, a typical side effect of that type.
The English dub of Yu-Gi-Oh! 5Ds gives Yusei Fudo a fear of bugs in Episode 2. This gave them some potential 40 episodes later, when his opponent had a deck full of spiders, including one really bigplot-related one. It's a mystery how they didn't realize that Yusei being scared of something like bugs is just... laughable.
Doraemon: The title character is afraid of mice despite being a robotic cat. It's because he was once sleeping and mice ate his ears. He turned blue of the shock and that's why he is a blue, ear-less robot cat.
General Blue from Dragon Ball in fact this is what breaks his concentration on paralyzing Goku when a mouse crawls across his leg.
In Pokémon, Dawn's reactions to Plusle and Minun (two mouse-like Pokémon) range from Blue with Shock to shrieking collapse. Oddly, it's just those two; she has no problem with other Electric Pokémon (like her own Pachirisu), or mice (like Pikachu and her Cyndaquil). It stems from a childhood incident that gave her an Embarrassing Nickname. She gets over it later on, though.
Rassha in Ruin Explorers. Inconvenient in that one of her traveling partners has a curse that turns them into a mouse whenever they do magic.
All the Saber Marionettes in Saber Marionette J except Lime. And it's hard-coded into their programming.
Katsuobushiman from Anpanman is a skillful samurai that's a master with his blade...but, thanks to being a dried bonito fish, he has a horribly crippling fear of cats. Baikinman has managed to use this fear against him, building giant feline robots. This also gives him troubles when being around Nyanja, a ninja cat.
Psychopathic Manchild Pierrot le Fou from Cowboy Bebop also hates cats, due to his association of them to his experimental trauma. It also turns out the cat that was present during the experimentation had heterochromia just like Spike has (his false eye doesn't quite match his real one), which makes him freeze up at a crucial moment during their final showdown and allows Spike to defeat him.
Every single mermaid, (except Masa), in My Bride Is a Mermaid is utterly terrified of cats, to the point that San's father (who is the head of a Yakuza clan) evacuates a school because Nagasumi had a kitten with him. Mikawa goes even further, using his contacts to bring in the military.
Gilbert from Pandora Hearts; he was terrified into freezing up by the mere presence of the Cheshire Cat, to the point where he didn't react when Cheshire was about to rip him wide open, and he didn't even look like a cat. Cheshire looked like a bishie in a cat costume.
Ranma from Ranma ½ developed this after training for a particular technique. Except there's a stinger in the tail — Ranma's fear can drive him into a temporary psychotic state where he becomes a mindless but unbeatable berserker, and only Akane can bring him outta his funk. What makes this worse is that one of Ranma's many fiances is cursed to turn into a cat when exposed to cold water.
Saiyuki: In the Saiyuki Party Drama CD Sanzo is terrified of a small kitten that Goku brings in from the rain, so much that when it hides under his kimono he starts screaming (in some fan's minds) like a sissy.
This is played with in the Reload anime with a mixture a fear and a supposed allergy. He got over it.
The wolf Toboe from Wolf's Rain says that cats creep him out. However, after the world's death and rebirth Toboe is seen in human form cradling a stray kitten.
Professor Chronos from Yu-Gi-Oh! GX was afraid of cats (and the fact that Daitokuji-sensei's pet cat Pharaoh was a constant presence at the Osiris dorm didn't help).
In Yu-Gi-Oh! ZEXAL there are two characters with this phobia: Astral and Rio Kamishiro.
Kim from Inubaka: Crazy for Dogs, due to being menaced by feral dogs on a regular basis during his childhood. He eventually gets over it and adopts a shiba puppy, Chanta.
Yōko from Inukami! has a fear of dogs, which one might think as strange, given that she's an Inukami (dog god) herself... except that she's actually a kitsune.
Shun Mitaka of Maison Ikkoku has an inconvenient fear of dogs. Problem is, the object of his affection (Kyouko) has a big dog she is really fond of, and his arranged fiancée (Asuna) has a whole bunch of them in all sizes. He beats his fear, by getting his own dog, who then gets him into a compromising (marriage) position.
Fujiko Mine from Lupin III is afraid of frogs. Naturally Lupin teases her from time to time about it, and Zenigata used it against her on one occasion to get information out of her. In another episode, Lupin actually uses a frog to knock Fujiko out, whereupon he ties up and gags her in order to steal her identity as part of a con.
Tetsuya Tsurugi from Great Mazinger and Kyouichi Shidou from Idaten Jump. Both of them were attacked by birds when they were small children. Naturally, the omake of the Idaten Jump episode featuring Shido's hate of birds milked it for what it's worth.
Sengyoku of Houshin Engi is afraid of birds after being stalked by a guy with birds.
Blue from Pokémon Special is afraid of birds for roughly the same reason. She gets over it by confronting Ho-Oh, the Pokémon who kidnapped her, and capturing Articuno, Zapdos, and Moltres, also known as the legendary birds. She then sics them on The Mask of Ice.
Slugs & Snails (molluscophobia)
Genie in Rune Soldier had some very bad experience with giant snails, which leads to Louie giggling immaturely and thinking of Naughty Tentacles.
The heroine of Slayers, Lina Inverse, also known (to herself) as Sorceress Genius and (to anyone else) as Bandit Killer, Dragon Spooker and Enemy Of All Who Live, is terrified unto death by two things: Slugs, and her big sister Luna. Her sister is also the reason why she fears slugs. Luna was pissed off because Lina decided to sell pictures of her in the bath, and...
Ferrets: Inori from Fresh Pretty Cure! is afraid of ferrets at first, due to getting bitten by a ferret whom she tried to tend to (she's a veterinarian daughter)... and then when she became a Precure, she got saddled with a ferret fairy, Tart, which freaked her out that she either communicates with her friends with a phone in the same room just so she doesn't need to look at Tart, and used a long range hand device for body contact. That got resolved in about 10 episodes after one "Freaky Friday" Flip in which Inori got stuck in Tart's body and made her overcome her fears.
Octopus: Miki from the same series is reduced into a screaming loon whenever she saw an octopus, living or not, due to an incident when she's young and tried to play with a small octopus, only for the octopus to wrap her hands with its tentacles and started showing off its tentacles in close up, freaking her out. Since she was trying to be 'perfect', she tried hiding this fear, but things excarbated when the current Monster of the Week is taken from an octopus statue. Thankfully, Setsuna managed to give blunt but encouraging words that eventually pushed Miki to get over her fear and fight the monster, and eventually her whole fear.
Kaitou Kid, the titular character of Magic Kaito and an Ensemble Dark Horse character in Detective Conan is afraid of... fish. To the point where only a bomb going off on a boat urges Kaito to scuba dive to find out what happened to his not-girlfriend Aoko and Silver during a chapter in Volume 1.
The titular character from Shinryaku! Ika Musume is deathly afraid of sharks and killer whales, even inflatable ones (in the beginning, at least). Justified in that she is a squid girl and sharks and killer whales are natural predators to her and since she has no idea what floats are, she assumes that the inflatable ones are real. She works and lives near a popular beach with lots of children...
In Pokémon Special, given how long she's been in the wild, you'd think someone like Sapphire wouldn't exhibit this. However, during the single-elimination tournament at the Battle Frontier, she winds up paired against Tucker and subsequently chokes when he deploys his Salamence (compared to Ruby, who went up against Emerald but threw his fight). Reviewing the R/S arc should give deep insight as to the source of this particular issue. And unlike Blue above, she hasn't had the chance to thwart this issue... yet.
Iris from PokémonBest Wishes has a huge fear of Ice Pokemon similar to Misty and her fear of bugs. The first Pokemon she reacted to do with absolute disgust was Trip's Vanillite, one of the most harmless looking Ice-type Pokemon around. When both Ash and Trip ask her why she's scared of Vanillite, she replies that as a Dragon trainer, she has developed an emotional bond for them including the weakness. Trip calls her out on it though because he says that Dragons are also super effective against each other and should have a fear of Dragons as well. Iris then tells him to shut up and quickly corrects herself by saying she can't stand the cold.
Vegeta from Dragon Ball Z is afraid of worms. He meets giant worms in Buu's body.
Flying (aviophobia) or Heights (acrophobia)
Gene Starwind (space travel) from Outlaw Star (Conveniently, the titular Cool Ship has Applied Phlebotinum that keeps the fear from taking effect). Rather justified because his last experience in space before the story begins saw him watching from an escape pod as his dad was killed.
Sailor Jupiter (her parents died in a plane crash), although apparently the writers forgot about it when they put her on a plane in an episode of the final season. (It was only mentioned in the manga.)
One villain in 666 Satan took this to a ridiculous degree: he's so afraid of heights that he is scared crapless if he needs to stand up.
Hayate the Combat Butler: Katsura Hinagiku was deathly afraid of heights, although she seems to be able to handle them now, particularly when it means spending time with Hayate, or something having to do with him. Ayumu also seems to have a similar effect on her.
Masayuki from Ghost Hound became deathly scared of heights for perfectly understandable reasons. He got over it by spending hours at a time playing a virtual reality flight simulator game. Actual flight didn't hurt either.
Tasuki of Fushigi Yuugi, who naturally is the first person overboard when the ship hits a violent storm. Additionally, vitriolic best bud Tamahome's preferred method of torment is dangling him over a body of water.
Any and all Devil Fruit users in One Piece have this to some degree, and with reason.
Ranma ½: Possibly Ranma, though it's less from actual fear of water and more from the annoyance of having his curse triggered. Ryoga definitely fears water, especially when Akane's around.
Golem in Monster Rancher hates water. Justified because he's made of rock and would sink like a stone.
Aiko of Ojamajo Do Re Mi. The story is that she told her dad that she could put her head in the water. Then, they have a contest to find out who can put their head in the water. She drowned 10 seconds into the contest.
Seine from Hekikai No Ai On since her second father tried to drown her. It took years to sit in a bathtub. It is also a disadvantage against the mermaid she fights, since they live in the sea, and Seine refuses to learn how to swim.
Rita Rossi, the Cute Mute from Ashita no Nadja, because her parents died in a huge fire that broken in their circus, and poor little Rita saw them perish..
Aoba from Durarara!! has a rather strong fear of fire. However, he uses this to his advantage in order to frame Izumi by setting his room on fire and making it seem like it was Izumi's fault because he forgot to unlit the cigarette he smoked. He plays this straight though after the events though.
Barnaby Brooks in Tiger & Bunny, due to the circumstances of his parents' deaths.
Other things in nature
Astrapophobia, Ceraunophobia, Brontophobia (fear of thunder and lightning) or Tonitrophobia (fear of just thunder): Haruhi from Ouran High School Host Club has this (these) fear(s), after being discovered to be afraid of little else.
Himawari on Wandaba Style has a fear of running out of air while in space, which is bad, since she and the other members of Girl Group Mix Juice are trying to get into space to perform a concert on the Moon.
Skuld from Ah! My Goddess is afraid of ghosts, which is surprising (and funny) considering that she's a goddess.
Sakura Kinomoto from Card Captor Sakura is afraid ghosts much to the point that even hearing a rumor or a ghost story frightens her.
The Action Girl Ran Mouri of Detective Conan. In her case, it's kinda justified: she fears them not because of the supernatural stuff, but because if she ever was under attack from them, her physical strength would be useless against them.
Hikaru Himuro from Dragon Drive also has that fear. Unfortunately, Chibi is a victim of his fear, as he grabs on to Chibi's tail for some reason (maybe a reflex to help calm himself?), and doesn't let go when he passes out from fear, much to both Chibi and Reiji's annoyances.
Liz Thompson from Soul Eater is afraid of ghosts. Not helpful when her job/homework requires her to fight them, and odd considering she's something supernatural herself.
In contrast, her death god teammate is afraid of completely mundane things - see 'Various'.
In the Naruto anime, when Naruto heard that one his missions has possibility of ghosts being involved, he curled into a ball which odd when didn't back down against the Kyuubi.
Jonouchi Katsuya from Yu-Gi-Oh! has such an intense fear of the supernatural in general (Ghosts included) that he actually passes out twice as a result of them — Once during the manga's version of an Amusement Park of Doom and again before his duel against 'Ghost Kotsuzuka'. He wins the duel after being woken up in the end.
Veronica of Franken Fran is an Artificial Human built for assassination and bodyguard duties. She also recoils in fear at the prospect of ghosts.
Cilan from PokémonBest Wishes has a huge fear of Ghost-type Pokemon. He tends to zigzag around this trope, because while he's not scared of the Ghost Pokemon once it shows itself to be the cause of items moving around, the mere thought of being around them apparently creeps him out. Special mention in BW029 when he freaks out and screams like a girl when the Litwick were controlling the items in the haunted mansion.
One Piece has Brook, who is terrified of ghosts, zombies, and all other things that can be considered spooky...which is about as outrageous as it gets considering the fact that he's a living skeleton.
Tsunade from Naruto, after her lover Dan died and she couldn't do anything about it. Should have been quite a cramp on her superninja-doctor career... until she overcame it during a high-stakes battle at a point of near mortal defeat, thus leading to overcoming her opponent Kabuto as well (this must be a trope somewhere).
Also Gaara when Sasuke punctured his chest and saw his own blood for the first time he freaks out.
Heart, from Fist of the North Star. Like Ranma, he flips out and becomes a berserker if he sees his own blood.
Naga the White Serpent from Slayers is also quite afraid of blood, since she walked on the place where her mother was assassinated, which was all blood-splattered.
Made even worse by how she killed the assassin... via using a Razor Floss-like spell, thus splattering the room in even more blood.
Ryuhi Kin from Ashita no Joe has an immense fear of this due to him accidentally killing his father when he thought his father was a hungry soldier coming back from the Korean War to get him food.
The male lead from Girls Bravo. Then his so-called rival (?) is terrified of men (arrhenphobia).
Yamcha from Dragon Ball. He wanted the Dragon Balls to actually cure this phobia, since he also wanted a girlfriend but was too terrified to ask any girl out. He got over himself after hanging out with Bulma, though.
At the beginning of the series, most (if not all) of the male cast of Vandread are scared of women. This is understandable, since one of the main plot points is that men and women have been segregated for years, to the point that neither gender really believes that the other exists anymore. To men, women have become something akin to horrible, frightening monsters of legend.
The Haou-Sou in Onidere are all afraid of the opposite sex, with two of them being male.
Urusei Yatsura: Shutaro Mendou is afraid of one specific woman—his fiancee, Asuka Mizunokoji. Due to her intense strength (she even tore a tank apart and made it into a makeshift armor suit with her bare hands) and athleticism (she could run 100 meters in 12 seconds with same armor suit—200 kg, or 440 pounds) a simple "light hug" from her causes multiple broken bones and internal injuries. Since Shuutaro is rather terrified of being crushed, it seems unlikely that this relationship will ever be consummated.
The doppelgänger who appears in early chapters of Rosario + Vampire Season II is very afraid of women. It doesn't stop him to kick their asses or copying them.
Urusei Yatsura has Asuka Mizunokoji, the sister of Tobimaro Mizunokoji. She's isolated according to the Mizonokoji family's tradition, from any and all males from the moment of her birth until the age of 16, at which time an omiai will be held for her to get married. As such, even her brother was unaware of her existence until then. Because of this isolation (and the fact the first male she met was the lecherous Ataru Moroboshi) she is extremely timid and deathly afraid of males. Now whenever she sees one, she pushes him away, screams "Eek! A maaan!" ("Aa~! Otokoo~!") and runs in terror at high speed from all males, not heeding any obstacles unfortunate to be in her path (such as buildings). She is, thanks to her daily training and the genetics she inherited from her mother, insanely strong (once tearing a completely armored tank apart and fashioning it into a makeshift suit of armor on herself with her bare hands), as well as very athletic (being able to run 100 metres within 12 seconds, while wearing her 200 kilogram suit of armor). While engaged to Shutaru Mendou at the omiai to end the Mendou-Mijunokoji rivalry, her strength even means a simple "light hug" from her causes multiple broken bones and internal injuries. It seems unlikely that this relationship will ever be consummated, as Shuutaro is rather terrified of being crushed.
In Girls Bravo, the eventual Big Bad Yukina has the same allergic reaction to men as the male lead Yukinari has to women. She's a Broken Bird as a result. She also has superpowers. It's not a good combo. In the last episode, she gets over it thanks to Yukinari and promptly becomes his (second) Stalker with a Crush. Unfortunately for Yukinari, he hasn't gotten over his phobia yet.
Shutaro Mendou of Urusei Yatsura is afraid of both the dark and tight spaces, though this was accidentally caused by locking his child form in a large pickling jar while trying to ''cure him of said phobias.'' As long as a girl's in sight, though, he's not claustrophobic as long as she can see HIM. If she CAN'T see him, often by putting a bell over him (and combining his phobias) he'll either break the bell out of terror-induced strength, or scream "It's cramped! It's dark! I'm scared!" over and over again until he is freed from confinement (as it often is in the anime).
Baikinman from Anpanman, being an alien bacterium, is terrified of soap. Contact with it reduces him to the size of a fly. Likewise, Mushibaikinman, a cavity from the same species as Baikinman is afraid of toothpaste, as it has the same effect on him. Interestingly, they're the only members of their species to have this weakness.
Also, Seychelles hate the cold to the point of collapsing in Cuba's arms after walking in the snow for a while, despite wearing a huge coat. Justified Trope due to the very warm Seychellois climate.
Sakaki from Azumanga Daioh is scared of horseflies, but also of thunder, earthquakes, and even the mechanical guards at construction sites.
In A Certain Magical Index, Hyouka Kazakiri is terrified of Touma Kamijo, despite him being one of the nicest guys on the planet and her having a crush on him. It is because she is an artificial angel, and she subconsciously sensed Touma's right hand, the Imagine Breaker, which would erase a supernatural being from existence on contact. When Touma learns this, he assures her that her fear is a good thing, because the fear of death proves that a being is alive. She somewhat gets over her fear when Touma saves her several times and assures her that he would never willingly harm her.
Goku from Dragon Ball Z is terrified of needles, this came after he got a shot after his first fight with Vegeta. Sorta justified: he had never gotten a shot in his life until then.
Miyuki Takara of Lucky Star really hates dentists.
Makoto Kenzaki from Doki Doki Pretty Cure is afraid of dentists in episode 35, but she overcomes her fear in the same episode.
Ryoshi Morino in Ookami San has extreme scopophobia (fear of being seen or stared at); he shrinks down into a cringing ball and covers his face whenever people look at him.
The Rurouni Kenshin anime gives Sanosuke a crippling fear of trains (which pops up in every Filler episode and Non-Serial Movie that involves riding a train), as well express a suspicion of cameras, fearing that it'll steal his soul.
Jesus in Saint Young Men has a phobia of salespeople, which he confesses to Buddha was the real reason for his famous freakout in the temple. Apparently he was trying to hide under the chair, 'used too much force', and when people rounded on him for an explanation as to why he threw the chair he was so berserk he screamed at them all about how this was supposed to be a place of worship.
In a Yu-Gi-Oh! GX 3-parter, it is revealed that vampires scare the crap out of Daitokuji-sensei. Guess who was the Villain of the Week in all 3 episodes? He may have been lying, however. He was secretly a member of the Seven Stars, a group that Camula also belonged to. They were only seen as a group in one brief scene (in shadow), and it is not known if the individual members actually helped each other at all.
In Ashita no Joe the titular character is afraid of hitting his opponents in the head, because of his rival Rikishi died by suffering a blow to the head by Joe himself.
It was hinted that Magellan, the main antagonist of the Impel Down arc of One Piece, was actually agoraphobic (the polar opposite of being claustrophobic) and was nervous in large, open spaces, enjoying dark, enclosed areas. (Likely a big reason why he was so suited for his job.)