Motoko Aoyama from Love Hina is afraid of turtles. So her fellow tenants adopt one that can fly.
Bachou Mouki from Ikkitousen is deathly afraid of snakes.
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!
During the "Knightfall" saga of Batman, the mayor of Gotham is revealed to have this fear (as revealed by Scarecrow's fear toxin). Joker, who is partnered up with Scarecrow, naturally exploits this for all it's worth by terrifying the mayor with a baby rattle (to remind him of rattlesnakes).
Susanita from Mafalda is terrified of turtles. Unfortunately, her best friend Mafalda is unaware of her phobia and invites Susanita to her house just to show her the family's new pet turtle, Burocracia. Cue Susanita cowering in a corner.
One episode of Kim Possible parodies Indy's fear. When Kim arrives in a spiked pit while searching an abandoned underground temple, she jokingly asks, "Where are the snakes?" When hundreds suddenly appear, she retorts, "I was just being sarcastic!"
Also parodied in at least one Tomb Raider comic. "I met this man once who would have been a good archaeologist, but he just couldn't get over his fear of snakes..."
Launchpad also parodies it in the Five-Episode Pilot of DuckTales: "Yah, a snake! I hate snakes! No... that's somebody else. I sorta like snakes." Then one nearly eats him: "Now I hate snakes."
In Jackass: Number Two, the gang does a bit where they trap Bam Margera in the back of a trailer with a (devenomized) king cobra. Hilarity Ensues when Bam goes apeshit and actually starts crying.
It gets worse in Jackass 3D: They set Bam up to do a prank... but are really sending him directly into a trap door that leads into a pit full of rubber snakes. Bam flips his shit. Then they add in REAL snakes, including a giant yellow one, and he proceeds to frantically hold on to the side of the pit, trying to pull himself out.
From Dusk Till Dawn star Salma Hayek has a real fear of snakes, and had always refused to be near them. When she read the script, she knew that her phobia would prevent her from taking the part of Satanico Pandemonium, but Robert Rodriguez conned her into thinking that Madonna was ready to take the part instead, so she spent two months with therapists in order to overcome this fear.
Snakes (especially the enormous constrictors that always crop up in Robert E. Howard's stories) are the only thing that Conan the Barbarian is afraid of, besides some displays of sorcery. The ancient god Set, the embodiment of evil in Howard's stories, is represented as a serpent.
The Conan RPG system has the spell "Dance of the Cobras", which is Exactly What It Says on the Tin. Cobras are hypnotized to circle a person, doing damage each round until the victim either dies from the damage or kills all four of the cobras, which are specified as at least Medium size. The spell comes from the Conan story "The Man-Eaters of Zamboula," which had Evil Sorcerer Totrasmek doing this to the Love Interest Zabibi, who is forced to dance for her life against the snakes.
Rincewind in the Discworld novels is afraid of almost everything, but ends up sent to the Snake Pit after he accidentally reveals to the Evil Chancellor that he "doesn't like snakes very much." Being Rincewind, he tries to cover up with "Well, I mean, some snakes are okay..."
Also, the Snake Pit was the only functional torture device at the moment in Al-Khali, despite the vizier being...well, what he is. And by functioning, we mean it contained one snake, who behaved much more like a Real Life animal and simply avoided Rincewind.
Kahlan, the primary female character of the Sword of Truth, hates snakes. She becomes highly nervous and uneasy when Richard mentions he saw snakes in the water, later has nightmares about a large snake wrapping around her legs. Her aversion to snakes is mentioned several times again over the course of the series. This is a fairly common syndrome among female characters from this series.
Josh Newman from The Secrets Of The Immortal Nicholas Flamel is revealed to be afraid of snakes. He lampshades it in The Sorceress - "Snakes! Why is there always snakes?" He even says the trope name in The Magician.
Hank the Cowdog from the series of the same name can face bobcats, coyotes, mad bulls, and wild horses (although he'd much rather not). Snakes are the only thing he's specifically named as terrifying him.
Silk, from the Belgariad is a victim of this. He also has a fear of caves.
An episode of Cops showed two policemen afraid to respond to a call from a resident who found a snake in his closet. The guy from animal control, on the other hand, had snake tattoos and couldn't believe the resident didn't want to keep such a pretty snake.
Terrorist Kelly Peyton on Alias is terrified of snakes and only gives important information to the CIA under interrogation when they threaten her with one.
On Home Improvement Tim becomes agitated when he learns that a harmless garden snake is somewhere in his house.
Eiji of Kamen Rider OOO mistaken the Eel Can-droids as snakes on first glance.
Wayne of Swamp Loggers expresses great unease about snakes. One could wonder about his choice of job.
An early episode of Adam-12 saw Malloy and Reed approach every white 1958 Ford convertible with trepidation ... since a stolen boa constrictor might be hidden in the trunk of one of them.
Subverted with Agent Scully on The X-Files. In "One Breath", her mother tells a story how she felt guilty for shooting a snake with her new BB gun. Although deathly afraid of snakes, she held the snake and it died in her hands, which is very weird as people with this phobia are grossed out with only pictures of snakes. When Mulder and Scully investigate cases involving snakes, she isn't exactly on edge ("Die Hand die Verletzt") and she even gets a tattoo of a snake eating its own tail in "Never Again". On the other hand, there are lots of snakes in "Signs and Wonders", but even Mulder who doesn't suffer from this phobia is very nervous around them.
The Spelunker from Spelunky, being kind of an Indiana Jones expy hates snakes, too. Doesn't really seem to stop him, though.
World of Warcraft has a shout out in the form of an NPC with a strong fear of snakes who's named Harrison Jones, which takes Indy's last name and his actor's first name.
The last line of a journal entry in Vesuvia that mentioned the discovery of a charred snakeskin was "Snakes - anything but snakes..."
Gemini Man from Mega Man 3 hates snakes. Not surprisingly, he takes massive damage from Snake Man's Search Snakes.
A certain side quest in The Lord of the Rings Online involves retrieving some baby turtles from the work shed of a hobbit named Grobo Dogwood who just so happens to be deathly afraid of turtles. When you go to pick up the little suckers, each and every one is called "Grobo Dogwood's Greatest Fear."
Yar, the lemur chief from Dinosaur apparently has a huge fear of dinosaurs. He eventually gets over it after a newly-hatched Aladar pees in his face.
In one episode of Doug, Roger is afraid of snakes.
Archer has three great fears. Two of them are alligators and crocodiles, to the point where he has memorized every single fatal alligator and crocodile attack in the United States. He would have memorized the ones in China, but their records are spottier.
Anime & Manga
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.
In the Spider-Man comics, Doctor Octopus once received such a beatdown as to develop this phobia. He had to be talked out of it in order to help Spidey with the current crisis.
Garfield was terrified of spiders early in the comic strips run. In more recent strips, he hates them more than he's scared of them, swatting them without even thinking.
In the My Little Pony: Friendship Is Magic fic Arachnophobia, PrincessCelestia has an intense fear of spiders. The plot is kicked off when Luna, following Celestia's advice to adopt a pet, brings home a huge spider whom she names Atticus. And just when Celestia is starting to adjust to Atticus' presence, his even bigger mate appears and freaks her out all over again.
Films — Live Action
The protagonist of Arachnophobia, a doctor who moves his family to a small town to escape the dangers of big-city life, only to come up against an invasion of deadly hybrid jungle spiders.
It's revealed in The Mark of Athena that when Annabeth (the main child of Athena) was younger, spiders used to swarm her when she slept and then scurry away so her father and stepmother wouldn't believe her. So it's not just a hereditary trait.
Ron Weasley of the Harry Potter series is deathly afraid of spiders, due to his brothers transmogrifying his teddy bear into a massive spider for a joke when he was much younger. During Harry Potter and the Chamber of Secrets, he and Harry end up having to "follow the spiders" into the Forbidden Forest. In the movie version, Ron quips "Why spiders? Why couldn't it be 'follow the butterflies'?"
In a fortuitous bit of casting, Rupert Grint, who plays Ron in the movies, is also deathly afraid of spiders. All of "Ron"'s expressions of fear in the movies are actually those of Rupert, since, according to the DVD special features, Aragog was animatronic. (Aragog's children, however, were CGI.)
"Ayatollah", the crime boss in Boris Strugatsky's The Powerless of This World, fears nothing except members of the class Arachnida. Unfortunately for him, one of the friends of his victim is commonly known as "Beelzebub, Lord of the Flies" for his amazing ability to control insects and spiders...
Giant spiders show up a lot in Tolkien's works, especially in The Hobbit and The Lord of the Rings. Among all other creatures in Middle-earth, nothing strikes more fear in the characters — especially the hobbits — than spiders (except for maybe the Balrog, which only scared the characters who knew what it was). Some people believe this stems from Tolkien having been bitten by a tarantula as a very small child, but he adamantly denied this in life.
The annotated edition of The Hobbit has a quote from Tolkien, in which he claims that he put the spiders in because he knew his son was terrified of them.
Peter Jackson also shared this fear, which he used during the film version of The Return of the King to make the scenes with Shelob as nightmarish as possible. He told the people in charge of CGI for the scene to keep enhancing things "until [he] couldn't stand it."
Adam Savage of MythBusters although in the Ultimate MythBuster special, Adam said his experience in the "Daddy Long-Legs" myth (arm stuck in a tube of spiders until one finally bit him) had gotten him over this fear.
Grant Imahara is also arachnophobic. And he gets the same type of "treatment" that Adam got...
Shane the Red Ranger from Power Rangers Ninja Storm. First mentioned by Tori to prove it's really her and not her evil clone, it turns up later in a surprisingly subtle fashion - a flashback of kid-Shane rescuing an alien ball of light from a spider-web.
Chief O'Brien once admitted to a fear of spiders in an episode of Star Trek: The Next Generation. He not only got over it in time, he actually kept a pet tarantula. Presumably Keiko told him to leave it behind when they moved to Deep Space Nine.
Various spirits from Ghost Master specialize in exploiting certain fears; one of them in a giant spider.
One of the quests that you can do in Stormreach Harbor in Dungeons & Dragons Online involves a guy named Berne Jorn who's been afraid of spiders ever since he was a kid. The quest he sends you on, which is called "Arachnophobia," has you clearing the eight-legged bastards (including a huge boss-level one) out of his family crypt.
Toonstruck's Drew Blank exclaims "Spiders! Why did it have to be spiders?" upon seeing a couple of them crawling on the wall.
Bounder Boffin of The Lord of the Rings Online is terrified of spiders, which you have to kill during the introductory instance for Hobbits in order to help him cut through Old Odo's Leaf-farm to escape a Black Rider.
Farkas, an otherwise fearless warrior in The Elder Scrolls V Skyrim, at one point refuses to go any further in a dungeon after encountering giant spiders there.
Tali in the Mass Effect series is apparently afraid of spiders, judging by her reaction to the Gestation Pods hatching if you should take her along on Grunt's mission in Mass Effect 3.
Justified in that not only does her home planet not have insect life of any kind (therefore presumably no spiders either), she and her people have lived on ships all their lives, and have had no real contact with anything that crawls or scuttles.
It's speculated that arachnophobia in humans is partially due to the perception that they're associated with filth and neglect. Quarians evolved without analogues to insects, but they also spread to some other planets, and vermin hitchhiking is certainly something that could have happened and would cause them distress.
Garrus also dislikes spiders, though to a lesser extent.
"If I never see another spider again, I'll die a contented turian. Unless they have spiders in the afterlife. Damn."
Girl Genius - Neither Agatha nor Gilgamesh want to rescue Zola from the "Nyar" spider, and it's not from annoyance with her setting off every trap available in the previous page. Even though one day earlier Gil alone defeated a mechanized army and she's getting ready to do much the same.
Gil:That was a small army. This is a big spider!
Shelly from Wapsi Square is generally very tough and more than willing to take on a mugger with a knife. However, show her a single spider and she'll be screaming for help.
As seen in this early 8-Bit Theater strip, spiders freak Fighter out. So you can just imagine what's going through his mind when this happens later on.
Simon (Honeydew) of the Let's Play/Yogscast makes his feelings about spiders quite clear, and squeals in hysterical fear whenever one appears in a game he and Lewis are playing. He'll quickly get over it, until another one ambushes him.
In an episode of Gargoyles, Elisa's mom, Diana, was faced with the spider god Anansi and his minions, causing her to say "Spiders! Why did it have to be spiders?"
In Hey Arnold Arnold's parents, who are homages to Indiana Jones, both have a fear of spiders.
Norman from Mighty Max. There is a possible nod to this in the introduction, where every encounter Max faces in the introduction is handled by Norman. The only encounter Max directly deals with himself is the large spider. This is at least partly to do with a prophecy that a spider would kill him, which happens in one of the final episodes. If you knew that was going to happen, wouldn't you be antsy around arachnids?
Most Steve Irwin fans found it simply hilarious that Steve could wrestle crocs, get unbearably close to cougars and bears, and handle venomous snakes, but he squirms like a little girl when a harmless spider crawls towards him.
British comedian Phill Jupitus is terrified of spiders — and irate about people who aren't afraid of spiders and use this fact to torment him.
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.
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.
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.
If someone like Indiana Jones can have a phobia, then it makes sense that other people who are as tough as he is can have them.
Atomic Robo's fear of bugs is not irrational. Oh no. Fearing icky, evil things that can crawl into your body and die and get their sticky bug guts all over your insides and make you gross forever is completely logical!
Films — Live Action
Continuing on the Indiana Jones theme, Willie Scott from Indiana Jones and the Temple of Doom has no problem around snakes, but once she discovers she's walking through a room covered in insects and other related critters, she practically freaks out. And she needed to cross the room in order to save Indy and Shorty from a Descending Ceiling. After much complaining, she does.
Zen from Chocolate goes into a screaming panic when exposed to flies. She's autistic, so she can't actually repress that reaction. It causes a lot of trouble for her when one of her targets turns out to be a butcher with extremely poor sanitation.
Groucho Marx as Captain Spaulding in Animal Crackers. After bragging about how brave he is, another character points out a caterpillar on his jacket and he immediately faints. The next Marx film, Monkey Business, has him brag that he's "whipped his weight in wild caterpillars", however, so this trait didn't carry between "characters".
Nicci of the Sword of Truth suffers from a fear of lice (pediculophobia), as a result of being repeatedly infested with them during her childhood in the Old World. Upon seeing a young girl who has a lice problem, she forcibly cuts the girl's hair and washes her head, then instructs her to burn her clothing and bedding.
Private detective Bobby Dakota, in Dean Koontz's The Bad Place, fears insects of all kinds.
The Star Wars Expanded Universe gives us the Dark Nest Trilogy, about...bugs from Alderaan. If you're around these bugs for a long enough time, you join their hive mind. Han and Leia's daughter Jaina, her boyfriend Zekk, and Luke's son Ben do so. Han Solo says "Bugs, why did it have to be bugs?"
In Galaxy of Fear, Zak Arranda has a definite aversion to large insects, which really bites him in The Swarm, which takes place on a world where the local people are giant bugs and the main threat is... smaller but still large bugs.
Adelbert Steiner in Final Fantasy IX, sort of. He's deathly afraid of oglops, an otherwise harmless insect.
Blathers the Owl from Animal Crossing hates bugs of all sorts, as made obvious by how he reacts every time you turn in something for the museum's bug collection.
Lyle Smithsonian of Metroid: Other M really hates bugs. Guess what's invaded the Bottle Ship?
Florina from Fire Emblem 7 is terrified by bugs (a support conversation shows her panicking when a bee flies around her), among a few other things.
Karol in Tales Of Vesperia is shown to be petrified of them when the party visits a forest teeming with insects. In a rare show of kindness, Rita gives him a can of bug spray, which becomes a skill called 'Bug Busters' for him.
Billy from The Grim Adventures Of Billy And Mandy is terrified of bugs of all kinds especially spiders. Things only get worse for him when he hatches an egg that contains a giant spider who thinks he's his dad.
Kim Possible bitches out Ron over complaining about a spider bite, however when a villain grows mutant cockroaches she has a very unKimlike freakout over how terrified she is of them. She's only okay with bugs when they're "little and flick-able." Ron on the other hand finds one giant Roach which acts more like a dog than a roach adorable and names it "Roachy".
Rod and Todd Flanders of The Simpsons are afraid of moths and ladybugs.
Big Guy T-Bone of the SWAT Kats is revealed to be afraid of bugs in the episode "The Ci-Kat-A". Watching a movie about killer space bugs didn't help. What emerges from a retrieved space capsule later in the day? Giant insectoid alien parasites.
T-Bone: Why did it have to be bugs? Razor: Just like that movie, T-Bone.
In the Danger Mouse episode "Aiaaagg! Spiders!", Penfold freaks out at a spider in the bathroom. Danger Mouse goes to take care of it, but the spider is much bigger than anticipated.
Buttercup's nightmare realm fear in The Powerpuff Girls episode "Power-Noia" is of spiders. Blossom goads her into fighting back.
Averted and subverted in Hyperion's series The Itsy Bitsy Spider (1993-95, USA cable channel, based on a 1992 theatrical short subject). Itsy is befriended by a little girl and is the target of fruitless pursuit and destruction by the little girl's teacher and a gung-ho exterminator.
Mice & Rats (musophobia)
Elephants, in many, many stories. Always played for comedy as the world's largest living land animal retreats in fear (or panics and destroys things) at the sight of a tiny mouse. Bizarrely, this one seems to be at least partly true. MythBustersdid it. It's speculated that it's because mice are big enough to be noticeable, but small enough that it's hard to keep an eye on them, particularly when they dash right between elephants' feet.
Exceptions: the baby elephant who makes friends with Jerry, and Dumbo. (The other elephants in Dumbo's circus certainly are, though.)
Anime & Manga
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.
Films — Live Action
The Chronicles Of Narnia star Anna Popplewell (Susan) was so afraid of mice that the scene where the mice chew through the ropes binding Aslan's dead body had to be filmed in two separate places; one with poor Anna and one with the mice.
John Rambo in First Blood. While having no problem with surviving in the wild and killing in self-defense, he clearly can't stand being surrounded by rats while hiding in a cave.
In Indiana Jones and the Last Crusade, it's revealed that Indy's dad is afraid of rats. (He says so when he encounters a horde of them in the Italian catacombs, and it is confirmed when he tells his father about it, causing the elder Jones to tremble in fear.) Must be a family thing (see also Indy's son being afraid of scorpions, above).
It makes sense. Indy's dad is a professor of Medieval studies and the bubonic plague which ravaged Europe in The Middle Ages was caused by fleas on rats.
Winston Smith from 1984 is terrified of rats, a fear which is used against him in the most horrible way possible in Room 101.
A short parody of this had the Ministry of Love turn out to be short of rats — and Smith wasn't scared of anything else they had to offer. He wound up actually trying to help them find a creature they could torture him with:
"If it's any help, I can't stand moths." "Moths?!" Esmond screamed. "What do you think we are, ruddy Harrods? We can't get moths for love nor money!" "Comes in here asking for moths," muttered Esmond's assistant.
In the novelization for Metal Gear Solid, it's hinted that Snake at the very least dislikes rats — having to be assured that there's only "harmless brown mice" in the Shadow Moses vent by Campbell is the strongest suggestion of this. How much of it is actually canon for the character is debatable.
Mord-Sith Cara of the Sword of Truth. Due to being harassed by rats while locked in a dungeon as a child, she becomes highly uneasy around them. Though she is able to stomach their presence a bit in the fourth book, her phobia is exploited and intensified when Drefen Rahl tortures her by allowing a group of agitated rats to claw at her stomach.
Gunn from Angel. First mentioned in S3's "Heartthrob", his phobia gets explicit illustration in S4, when the coming apocalypse causes a house's walls to fill with rats.
In the Are You Afraid of the Dark? episode "The Tale Of Watcher's Woods", a girl is captured by three witches and put in a wooden cage. One witch asks her if she'd like to "play with some rodents" and proceeds to put a bucket of rats into the cage with the girl, who happens to be terrified of rats. The girl then freaks out and says: "Why did it have to be rats?!"
The Brady Bunch: Alice is revealed to be afraid of mice in "The Impractical Joker" after seeing a small, white mouse running loose in the house. The mouse was on loan to high school freshman Greg for a science project, and Jan – playing up her one-episode practical joking side – lets the mouse loose.
Doc Robbins from CSI: Crime Scene Investigation, who yells and screams and generally stands there scared to death when a rat launches itself out of a body on his table. Grissom is left to chase it and watch it escape.
Topher in Dollhouse which Dr. Saunders/Whiskey takes advantage of.
Knit Knots on Imagination Movers seems to be at least somewhat afraid of Warehouse Mouse, telling the Movers to keep the "furry, woodland creature" away from him.
Ive Got A Secret: The first celebrity guest, Boris Karloff, reportedly had a rather mundane secret: "I'm afraid of mice." It wasn't long before the celebrity guests – at least during the CBS run – had more elaborate secrets to share.
Kenan And Kel: Kenan freaks out at the sight of a rat in his workplace. Kel, on the other hand, likes the "cute furry little mouse" Wendell.
The warden in one episode of The Mentalist is afraid of mice/rats. What does Jane do? He uses a muffin and some other tools to catch a mouse/rat, and as part of his plan to break out of jail, essentially scares the crap out of the warden so he won't stop him.
Gary from Miranda is scared of mice, and jumps onto a chair when told there's one in Miranda's flat.
Lady Penelope from Thunderbirds; otherwise she's a formal, impossibly-calm British spy.
One comedian recalls a time when his wife called him home and he was terrified because she didn't elaborate on the phone... and then finds her standing on a stool, holding a baseball bat, because there's a mouse in the kitchen. And she's telling him to kill it. When he refuses, she brandishes the bat at him and says in a threatening voice, "Kill it!"
The Good Fairy in Ceville. Obviously you have to exploit her weakness to solve a puzzle.
Zelda from The Legend of Zelda: Spirit Tracks doesn't like mice. Used as a gameplay as Link has to get rid of those rodents before she will move on. Understandably it comes up as the third part of the final boss fight where if she gets touched by one, she fall under Cole's control. This creates the amusing sight of an imposing suit of Animated Armor (which Zelda possesses) shivering in fear at the sight of a mouse.
The title character in Nick Chase and the Deadly Diamonds announced at one point that rats were his one weakness, his Achilles' heel.
In the Batman comics, the Scarecrow has developed chiroptophobia following years of defeats at the hands of Batman.
Films — Live Action
Ace Ventura, as revealed in the second movie, when the sacred animal of the Wachatis turns out to be one.
When Alfred asks Bruce Wayne why he uses the bat as his symbol in Batman Begins, Bruce responds, "Bats frighten me. It's time my enemies shared my dread." This fear is also present in his initiation into the League of Shadows, his first encounter with the Scarecrow, and when he first finds the cave and is surrounded by swarming bats.
Interestingly, in Batman Forever he specifically says that a vision of bats only scared him at first.
In the same movie, The Riddler reacts with absolute terror after being beaten by Batman, going so far as to envision him as the same bat that young Bruce saw flying toward him as a child (a result of having used The Box to map Bruce's mind and learn his Secret Identity).
In some versions, Scarecrow himself has a fear of bats owing to his encounters with Batman.
Hank Hill from King of the Hill is deathly afraid of bats in one episode, going as far as locking Bobby in the garage with a bat!
Pinkie Pie of My Little Pony: Friendship Is Magic might qualify; no less than one episode after singing a whole song about how she laughs at her fears, she freaks out when she mistakes a pair of tickets that landed on her nose for bats, somehow.
As an incredible irony, the Scarecrow apparently had this phobia from the start of his career in in Batman The Animated Series. In the first episode where he appeared, he claimed that his fear serum caused a victim to envision his greatest fear. So what does it cause him to see when he is exposed to it by accident? Horrible, demonic bats.
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.
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 ˝ 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.
Every single mermaid, (except Masa), in Seto no Hanayome 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.
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.
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.
Yuki from the first Juon has a huge phobia of cats, and is unable to even look at her friend Kanna's collection of cat ornaments and toys. Naturally, Toshio'sghostly cat companion, Mar, uses this to his advantage.
Subverted in Matilda. Ms. Trunchbull freaks out when she sees a black cat- and eventually kicks it. Matilda asks Ms. Honey if Ms. Trunchbull is afraid of cats. Ms. Honey replies "only of black cats- she is very superstitious".
In The Black Cat with Bela Lugosi and Boris Karloff, Lugosi's character reacts violently to the sight of a cat. His fear only serves a purpose in one scene in the middle of the film. Mostly it makes the character even more unlikeable, as if Lugosi needed the help.
Skylar Korman, an 18-month-old cared for by the members of The Baby-Sitters Club, has a deathly fear of "tats". Her fear is triggered by someone speaking the word "cat", a babysitter affectionately calling her "kitten", and small (cat-sized) dogs.
Rei Tachibana/Dyna Pink from Kagaku Sentai Dynaman. The mere sight of cat just freaks her out and she's rendered mostly incapable of fighting a cat monster, and it gets worse when said cat monster just transform the Mooks into cat statues. Ironically, she wants to develop a tool to communicate with animals... but can't even touch a cat without freaking out.
Ed in Flashpoint, at least according to Greg. Ed claims it was just once with a "scary cat," a point which Spike (hilariously) backs up.
Serge from Chrono Cross was said to have this (though he's apparently grown out of it by the time the player controls him). Justified in that he was attacked and nearly killed by a panther demon as a small child. We learn later that Serge's father, Wazuki, was turned into a cat-like form by FATE because that was the thing that Serge feared the most.
Splinter has this phobia in Teenage Mutant Ninja Turtles 1987, and you really can't blame him, seeing as he's a rat. His worst fears are realized when one of Shredder's experiments turns April into a feral Cat Girl who fails to recognize him due to the stress of the transformation.
Peter Griffin of Family Guy is extremely freaked out by "that weird stretchy leg thing that cats do when they lick themselves."
In one episode of The Powerpuff Girls, the Professor starts dating Ms. Keane, but when he finds out she has a cat, he's quickly turned off, saying he doesn't like them bacause of a "bad experience" he had with one. (He's probably talking about the episode where he was brainwashed by a cat-villain, although this is strange, seeing as he supposedly forgot that the incident happened at the end.)
Napoleon was scared of cats. Maybe if his enemies knew that, he would have been defeated after his first battle.
It wasn't without malice that Ches was made into a scapegoat in Tim Burton's 2010 version of Alice in Wonderland; Burton really hates cats. (Whether this is a phobia or not depends on who you believe.
Kim from Inubaka, 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.
The Professor in Nichijou is scared of dogs because she's afraid they may bite her. Rather amusing, given her favorite animal is the shark.
Sakamoto is afraid of dogs too, but that's mostly because he's a cat.
Sayo in Onidere cowers in fear of even the smallest puppy.
Tamaki of To Heart 2 is so afraid of dogs that she freezes on the spot. It becomes a major plot point in the original Visual Novel to save her from one.
To Love-Ru has Oshizu, who has a crippling fear of dogs, despite being a ghost. The characters point out that the dogs cannot do anything to her, as she's already dead, but it doesn't help.
Justified now that she does have a physical body to inhabit and dogs can now do something to her... and she is definitely aware of this, and it only makes her fear worse.
In The Gray Chronicles, Gray has a crippling fear of dogs. This is initially Played for Laughs as he's fearless when facing demons, monsters, and angry ghosts that are far more dangerous than a barking chihuahua. Then The Rival sent his vicious attack dog after him and it became outright horror. Later subverted when Gray takes in an injured puppy out of kindness and realizes not all dogs are evil. (He still names the tiny Scottie BLOODFANG THE DESTROYER!, but it's tongue in cheek, especially since the dog's the runt of his litter.)
Goblins in Pathfinder are psychotic little pyromaniacs who think little of charging into a village full of armed humans twice their size. While singing catchy tunes, no less. But they are terrified of both dogs (not wolves, who they will even train and ride) and horses. These animals seem to hate goblins on sight, and will attack without mercy. Eliminating them is step one in planning a successful raid.
A short time into the events of Geist, it is revealed that Big Bad Volks's Dragon Rourke is afraid of dogs. Close to the end of the game, Volks holds a meeting behind locked doors and gives specific orders to shoot anyone who comes close who isn't himself or Rourke. The solution is straightforward: possess Rourke. To possess someone, you must first terrify him. Thus, you undergo a series of short missions for the sole purpose of getting a dog into the same room as him.
Alessa Gilespe from Silent Hill was terrified of dogs, which due to her and the town itself being a Reality Warper who brings fears and abstract concepts to "life" is responsible for several monsters you see throughout the series; Split Head, Groaner, and possibly the Caliban.
According to the Drama CD of Guilty Gear XX, Zappa is terrified of dogs (then again, he seems to be scared of everything). Guess what? One of the ghosts possessing him takes the form of a huge, hulking black dog.
Frederick from Fire Emblem: Awakening is afraid of wolves due to nearly getting killed by one when he was younger. Even something that looks like a wolf, like a taguel, can trigger this.
One of Cerise's opponents from Magick Chicks is afraid of dogs, so once Callie, Cerise's new girlfriend then, lets that fear be known, Cerise casts the "Inifipuppy" summon that launches a lot of cute little puppies to the field. The puppies swarm her opponent and cause her to collapse into a fetal position.
Anya from Buffy the Vampire Slayer. She dressed up as a bunny for Halloween ("Bunnies frighten me."), sang about bunnies in "Once More, with Feeling!", then was standing on a table when misspoken incantations had filled the Magic Box floor with rabbits of all shapes and sizes, calling it a "cotton-top hell". Somewhat justified, in that a highly traumatic incident involving an unfaithful husband, angry villagers, and rabbits was the catalyst for her becoming a demon in the first place.
Bishop Brennan in Father Ted — apparently he was once stuck in a lift in New York with about a hundred rabbits, and "they began nibbling at my cloak and everything". Obviously he is destined to wake up in a room full of rabbits in "The Plague" episode of season 2.
Julius is terrified of rabbits on Everybody Hates Chris because he saw a horror movie about them when he and Rochelle were dating. When he takes Drew to a magic show, he passes out when the magician pulls a rabbit out of his hat. Clearly, he saw Night of the Lepus.
Madison in Power Rangers Mystic Force. She actually says "Why did it have to be frogs?" when facing a Monster of the Week planning to unleash poisonous tadpoles on the city — though many episodes earlier, she'd been able to overcome this long enough to kiss a helpful frog, turning him into their Sixth Ranger. This fear was carried over from her Magiranger counterpart, Urara.
Cornet of Rhapsody A Musical Adventure suffers from this. Unfortunately, frogs are hiding in every other container in the Marl Kingdom. Oh, and there's a kingdom of bipedal, sentient frogs.
Volgin from Metal Gear Solid 3. The phobia is so strong that if you toss a live frog at him during your boss fight with him, he'll stop attacking you to kill the frog, allowing you to get a hit in.
Lucca of Chrono Trigger. Becomes awkward when it comes up immediately after they meet with one of the party members, a giant anthropomorphic frog.
Refia of Final Fantasy III has a fear of frogs, which makes for a fairly amusing conversation the two times where you have to transform into one to enter a dungeon. It's even better if she is the character who has to cast the "Toad" magic.
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.
Scarecrow, the Master of Fear and Lord of Despair, is sometimes depicted as having a crippling fear of birds, explained by some writer's description of creative abuse on his grandmother's part. Makes sense — who wouldn't want their alter ego to be the thing that scares the thing that scares them?
A Deadpool comic involving him trying to join the X-Men included him continuously pestering Domino to find out what's her greatest fear; turns out it's chickens. While this seems to be a Big Lipped Alligator Moment for most of the arc, at the end where Domino and Wolverine are tracking Deadpool down they have to go through an air vent occupied by a chicken. Domino will probably Never Live It Down that a chicken took her out of action in a fight.
In Rango, Rattlesnake Jake is deathly afraid of hawks since they are his natural predator. Rango uses this to his advantage by getting the moles and their bats to ride in formation resembling a hawk. But Rattlesnake Jake figures out the ruse quickly.
In Stephen King's novel It, the frightening forms IT takes on, drawn from the personal fears of its victims, include giant birds in several cases, though IT is usually more remembered as a Monster Clown.
One character's fear of a giant bird is revealed later in the book to originate from being attacked by a normal-sized bird when an infant. The other does not fear birds per se, but the impossible dimensions of this one in particular, a species that does not and cannot exist in the real world.
Also shows up in the Neil Gaiman novel Anansi Boys, although is it an irrational fear when the birds really are out to get you?
A minor character from Harry Potter and the Chamber of Secrets, Mrs. Mason, is terrified of all kinds of birds, so when an owl flies in to warn Harry about using magic.... well, let's just say Uncle Vernon didn't get the big paycheck he wanted. Likewise, Harry gets locked in his room for the remainder of the summer.
Sheldon of The Big Bang Theory shows a fear of birds in one episode. After trying to ignore a bluejay (actually a black throated magpie jay), build a sonic emitter to scare it off, and finally donning a Boba Fett helmet and trying to shoo it away for good, it flies into the apartment, and makes it's home on Sheldon's couch. He gets over his fear eventually, to the point of naming it Lovey-Dovey.
He mentions that he became terrified of birds after a bird attacked him and stole his food as a baby, and when he was a child, a chicken chased him up a tree.
Hodges in CSI: Crime Scene Investigation reveals to have this when it came to processing a blue-and-yellow Macaw; he was terrorized by Canadian geese as a child while visiting an uncle in Saskatchewan.
Gueničvre in the French series Kaamelott is afraid of birds.
Hamilton "Ham" Dewey, from the series Saving Grace, is terrified of birds. He becomes agitated at a crime scene when he catches sight of the victim's small pet bird; later in the episode, his friends change his work computer's wallpaper to a close-up image of a baby bird's open mouth, which has him leaping back from the desk when he jiggles the mouse to deactivate the screen saver. His comrades also scatter birdseed in the courtyard just outside the squad room to attract large numbers of wild birds for the express purpose of freaking him out.
GLaDOS comes to hate them in Portal 2. To be fair, during her stint as a potato, one picked her up against her will, escorted her to its nest and started pecking at her, so she has good reason to be distrustful.
One episode of Total Drama Island shows that Tyler is deathly afraid of chickens. This has him voted off the island, and on the boat of losers, he sees dozens of chickens and freaks out.
David Boreanaz has a phobia of chickens. It made the Bones episode "The Tough Man In The Tender Chicken" rather interesting behind the scenes
Bea Arthur also had a chicken fear. The Golden Girls scene where Rose brings home a live chicken had to be restaged to make things easier on Bea.
Slugs & Snails (molluscophobia)
Anime & Manga
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...
Genie in Rune Soldier had some very bad experience with giant snails, which leads to Louie giggling immaturely and thinking of Naughty Tentacles.
Ursula of Breath Of Fire IV is utterly terrified of sea lice (a harmless bug). Especially hilarious as this ends up being revealed in a "What Do They Fear?" Episode segment between her and Nina, and Ursula is normally a Type A Tsundere who tries to be tougher than most men...
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.
When Aquaman's sidekick Aqualad was introduced he had icthyophobia (fear of fish). Since he was Atlantean, this was a problem.
This trope was discussed by Scarecrow in The Batman Adventures Annual #1. He has tied up a student and is using his Fear Gas to simulate him being covered in different animals, while lecturing him about how different people respond to different types of fear. The man is made to believe he is covered in snakes, spiders, and rats, and reacts stoically. Then Scarecrow tries leeches, and he goes into an instant panic.
Films — Live Action
Quinn, in the obscure horror movie Devils Den, is terrified of squirrels. He would prefer death by mauling by a mountain lion over an encounter with squirrels.
It wasn't a coincidence. Rita created the monster on purpose when she found out about it, and used a curse that amplified his phobia. By standing up to it, he not only broke the curse, but overcame the fear permanently.
Comedian Russell Howard is afraid of guinea pigs, shown by his reaction to a guinea pig appearing on Russell Howard's Good News when he unsubtly hid behind the guest animal psyhic.
Monkeys (maimouphobia) — Ron from Kim Possible. Especially difficult given the recurring monkey-themed super villain Lord Monkey Fist. For further irony, in the episode introducing Monkey Fist, Ron is granted the Mystical Monkey Power the villain sought.
Twister from Rocket Power develops a fear of giant monkeys in one episode.
Gorillaz singer/keyboardist 2D is deathly afraid of whales. As of current canon he's being held prisoner in a small underwater cell with a whale lurking outside the window.
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.
Cutter, chieftain of the Wolfriders and main character of the storyline, in ElfQuest. The revelation of this phobia is a significant plot point, midway through book one in the series: Cutter is required to 'fess up (from his subconscious, even) his worst fear specifically so he can be compelled to face and defeat it. Oh yeah, and there's also his rival Rayek and his fear of losing, but eh, who cares about him.
Bigby Wolf from Fables really doesn't like heights (since his ancestors weren't apes, he says).
Wolf in Marvel's Team America, but at least he can be kept conscious for a flight, although his powerful terrified death grip is hard on the seats.
Films — Live Action
Lt. Kaffee in A Few Good Men says that he gets sick when he flies because he's worried about "crashing into a large mountain."
The strongest and the most badass members of recon platoon in Heartbreak Ridge are both afraid of heights. On a parachute jump, the badass comforts the big guy thusly
Sergeant Highway: Jumping out of a perfectly good aircraft is not a natural act, so let's do this and do it right.
In Star Trek, Bones reveals that he suffers from a "fear of dying in something that flies!"
Bones: Don't pander to me, kid, one tiny crack in the hull and our blood boils in 13 seconds. A solar flare might crop up and cook us in our seats. And wait till you're sittin' pretty with a case of Andorian shingles. See if you're so relaxed when your eyeballs are bleeding. Space is disease and danger wrapped in darkness and silence.
Kirk: Well, I hate to break it to you, but Starfleet operates in space.
Most of J. R. R. Tolkien's hobbits are stated to be uneasy if they are any distance off the ground, this perhaps being one of the reasons why they live in "hobbit-holes" and one-story houses.
Tortall Universe: Keladry of Mindelan is terrified of heights after being held over the edge of a tower by her brother. It mostly goes away at the end of the second book, but never completely.
Jack Ryan, from The Hunt for Red October, not only lost both of his parents to an airliner crash, but early in his (aborted) military service the helicopter he was riding in, for an exercise, crashed, leaving him needing significant surgery, and ultimately having a fear of flying. He eventually got over it later in the Ryanverse series, though.
Percy Jackson in Percy Jackson and the Olympians is scared of heights. Justified in that he is a son of Poseidon, and the sky is part of the sphere of influence belonging to Zeus. The only exception is with Pegasi, because Poseidon created horses, which means that they are neutral territory.
Ironically, Thalia is deathly afraid of heights, despite being the daughter of Zeus.
Word Of God also says that children of Hephaestus are afraid of heights and falling, because when he was born, their father was chucked off Olympus by Hera.
In Discworld novels, Rincewind was always afraid of heights, so during his adventures he often ends up hanging or falling from high places. In Interesting Times his friend, Twoflover reminisces the "good old times":
Twoflover: Hey, do you remember the time when we went over the edge of the world? Rincewind: Often. Usually around 3 AM Twoflover: And that time we were on a dragon and it disappeared in mid-air? Rincewind: You know, sometimes a whole hour will go by when I don't remember that.
Actually, when he was on a boat, Rincewind clarified that it wasn't so much heights he feared as depths, which included large bodies of water. Anything where you could fall for a considerable distance, ending in death.
Anthony Horowitz' Scorpia has this for the book's Dragon, Nile, as his only weakness, the only thing that made him finish second at the training camp for the book's eponymous Murder, Inc.. It's also what leads to his death: under orders from his boss, he confronts Alex on a hot air balloon. Alex points out the height long enough for him to lose his focus, and a quick trick has him fall off.
In the "Hammer Drop", we find out that Jamie Hyneman apparently has a mild case of acrophobia. This comes up again in the "Outtakes Special". In some unaired footage from "Plywood Builder", Jamie is trying to reassure Christine about her impending (until she decided not to) zipline ride, and says "You know I'm afraid of heights". And he jumps off a building in "Dumpster Dive" ... but you could tell he wasn't happy about it. He was even less happy about crossing a 100-foot duct tape bridge 50 feet above the ground. Though, considering how unstable the thing was...
Colleague Tory Belleci is also acrophobic, so he had to go up in a stunt plane for the "Cold Feet" myth.
Supernatural's Dean Winchester is terrified of flying. Why do you think he drives everywhere?
MacGyver, at least in the early seasons. He seems to get over his problem with heights as the show progressed.
Sam Beckett from Quantum Leap, who, due to the amnesia caused by leaping, didn't remember his fear of heights until he leaped into a trapeze artist in the middle of a practice.
Both versions of Neverwhere have Richard Mayhew say he dislikes heights rather early on. The series has it in the introduction of the very first episode, where Richard talks about himself including his dislike of rats, blood, and heights. He encounters all three.
Daniel Jackson from Stargate SG-1 mentions in a throwaway line in one episode that he has a problem with heights. This came up right before he and Sam had to crawl across a tiny strip of floor over an apparently bottomless pit. He did fine with it, and eventually threw himself off their "bridge" to save their companion, 'cause he's Daniel.
Presenter James May on Top Gear gets height vertigo (a spinning sensation when he looks down from a height). He took flying lessons and acquired a private pilot's license to help himself learn to cope with it.
Alice from Alice is very afraid of heights. Most likely to balance the fact that she is an Action Girl.
Clark Kent in the early seasons of Smallville. Insert clever one-liner about "Irony" here.
On Cheers, Carla is afraid to fly, which prevents her from seeing her husband, hockey player Eddie LeBec, on the road. She takes an aviaphobia group therapy class conducted by Frasier on a plane to get over it. Carla overcomes her fear but Frasier suddenly becomes freaked out about being on a plane.
The first episode of The Bob Newhart Show has Bob heading a workshop for people trying to overcome their fear of flying. When the group is ready to "graduate", he plans a group flight from Chicago to New York, and enlists his wife Emily to join them...only to discover that she's afraid of flying herself.
A Sanford and Son episode has Fred inheriting money from an uncle, with the hitch being that he has to fly home to St. Louis (which he's afraid to do) to collect.
Jack Carter of EUReKA has acrophobia, although not to a disabling point, it does make him visibly uncomfortable in a few episodes.
Dave Barsky of Dirty Jobs, as shown in the "Aerial Tram Greaser" episode.
At least one team a season on The Amazing Race. If a fear is expressed at any point during the seasons (generally heights), expect the racers to have to face it at some point.
Reid's mom (played by Jane Lynch) in Criminal Minds mentions being afraid of planes.
Horatio Hornblower: Horatio is prone to sea-sickness and is really afraid of heights. Excellent material for an officer in the Navy, wouldn't you say? His fear of heights is referenced quite often, and he has to climb in the riggings or on the fighting top and deal with shortening sails quite a lot. In "Retribution", he volunteers himself to descend from a cliff on a rope and his pal Archie mischievously reminds him of his anxiety.
Archie Kennedy:[saucily] I remember when you used to be scared of heights, Mr Hornblower.
Horatio Hornblower:[measures the height he must descend from] Nothing's changed, Mr Kennedy.
John Mackey wrote "Turbine" to deal with his fear of flying.
"[...] But in the back of my mind, I'm always aware that we're up quite high — and our lives (and that beauty) depend on these massive pieces of machinery. If that machine (in this case, the percussion) should fail, we'd all be in serious trouble, so I just keep my knuckles gripped to the armrest, look out at the clouds, think pretty thoughts, and hope that the pulse of that engine never lets up."
— Mackey, in his commentary on the piece
Rey Mysterio has admitted in several interviews to being terrified of heights. It hasn't stopped him from jumping off something high yet, but he's oddly specific about it...
Grizzler of the Werebears toy line is very afraid of heights and transforms when he's up on a very high place.
Alister, Lara Croft's Non-Action Guy partner from the Tomb Raider series, does not like heights. At all. They make him "positively nauseous," as he comments at one point in the Japan mission of Tomb Raider Legend where Lara is making a dangerous climb up a really tall office building.
Blaze the Cat from the Sonic Rush series is often implied to have a fear of heights, especially when they reach a zone like Sky Babylon.
Emma, Hal's sister in Metal Gear Solid 2 doesn't like heights when asked about it by Raiden, but stated it's preferable to Water.
In Metal Gear 2 Solid Snake, Solid Snake can't be made to jump off the Tower Building in Zanzibar Land unless you first equip the cigarettes and leave him long enough for the smoking Idle Animation to start — presumably to soothe his nerves.
Bartz Klauser in Final Fantasy V has a fear of heights ever since he almost fell down from the roof of a two story house while playing hide and go seek.
Chrono Trigger has the example of Golem Boss who, after Dalton summons on top of the wing of an airship, cowers in fear from the height, without attacking. If not killed quickly, he then runs away.
All playable lawyers, save Mia Fey seem to suffer from this in the Ace Attorney series: Miles Edgeworth (who already has a Seismophobia to boot) needs Gumshoe to fetch him books from the higher up shelves, Phoenix Wright has to be led by his hand by his teenage sidekick when passing a bridge and breaks out into hysterical catchphrase-shouting upon boarding a Ferris Wheel and Apollo Justice can't ascend as much as 10 meters without starting to shiver like a dry pile of leaves.
In one mission in Grand Theft Auto IV, Niko seems nervous about having to take a lift on the outside of a building to get to its roof.
And in San Andreas, Cesar refuses to get into a crane because he's afraid of heights.
Brad Jones, The Cinema Snob, is terrified of flying. Linkara mentioned Brad had to knock himself out to get to Reno.
Red vs. Blue: Humorously, the biggest, baddest, meanest Freelancer of them all, Agent Maine, doesn't like heights. It comes up when they use a pulley to get something up to the roof of a building, and Maine's the only one heavy enough to counterbalance it.
Maine: Too high.
Carolina: Oh, don't be a baby. [kicks him out the window]
Sarge is also afraid of heights. Simmons points out that Sarge used to jump out of airplanes earlier in his military service.
Sarge: And how do you think I developed that fear?
Silverbolt, of the Transformers, is the commander of the Aerialbots. Just in case you can't parse the name: he transforms into a Concorde SST.
Lampshaded in that the reason Optimus Prime made him commander of the Aerialbots was that Prime knew Silverbolt's worrying about their safety would keep his mind off it.
In one episode of Rugrats, Chuckie develops a fear of heights after accidentally climbing the big kids' slide and finding himself way too high for his liking.
The concept is played in an XKCD comic of a man who couldn't go down a slide because it looked so tall. As an adult, he revisits it, and is surprised to realize the slide really WAS that tall.
Avatar The Last Airbender: While not quite so extreme as to be a fear, Toph explicitly has a strong dislike for flying, because lack of contact with the ground leaves her fully blind.
Before Mabel cured him, Grunkle Stan from Gravity Falls had a major fear of heights, to the point where he refused to allow a ladder in the house.
Marc Clark of The Amazing Spiez though whether it was a Compressed Vice is debatable since he had no problems with flying (in fact, he tends to fly the team's jet) and the problem was gone by the end of the episode.
Buster:(while on a plane) I hate flying, I hate flying, I hate flying, I hate flying...
Filmmaker Lars Von Trier rarely moves far from the border of his native Denmark, and has never left Europe due to an intense fear of flying. He even turned down an offer to direct for Steven Spielberg due to this.
Stanley Kubrick also had a fear of flying, and as a result, spent the last 40 years of his life in England.
Former soccer player and now sports coach Marcelo "Bichi" Borghi is also infamous by his fear of planes. The very few times he doesn't travel by bus/train/car with his teams, he has to be sedated to the point of almost passing out when on the plane.
Legendary American Football announcer John Madden was famous for his aviophobia. This gave him his iconic trademark - the Madden Bus.
General of the Air Force Henry "Hap" Arnold was one of the first military aviators, and would eventually rise through the ranks to become the first (and only - the 5-star ranks were discontinued after World War II) General of the Air Force. He was also afraid of flying, due to being one of the first military aviators to be in a plane crash.
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.
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.
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.
In Freddy vs. Jason, Freddy is frustrated by finding out that Jason is invulnerable even in his subconscious, until he finds Jason's one buried fear: water. Considering that Jason's initial death as a little kid, which sparked off his entire series, was by drowning in Crystal Lake...yeah.
One of the Mogwai rules in Gremlins: Never get them wet.
In Gremlins 2 The New Batch, Brain Gremlin dies in the same way as the Wicked Witch of the West does. He must be afraid of water, too.
Chief Brody from Jaws is afraid of water. And a good deal of people after having seen the movie, for that matter.
Susie, the little daughter of the hero in the original version of Piranha. With very good reason, in this case. Although when the piranha attack the camp she's attending she swallows her fear to try and save two of the camp counselors - she manages to rescue one of them...
In Terry Pratchett's The Colour of Magic, we meet dedicated "hydrophobes", who are raised with a deathly fear — indeed, loathing (not hate, which is the opposite side of love) of water. This fear is so strong that they can pilot a hovering board over the ocean, since their aversion to water forces it away from them. Unfortunately most of them end up dying early, overcome with revulsion over the water in their own bodies.
David Eddings features one particular character in the Belgariad / Malloreon series: Queen Layla of Sendaria. She has not so much aquaphobia but a specific form of megalophobia (fear of large objects): she is terrified of ships (more specifically, ships sinking), to the point that she can actually faint if a ship moves the wrong way.
Oddly enough, Data, the android of Star Trek TNG fame, gained a fear of water during the novelisation Metamorphosis in which he was turned human. (Yeah, it's that kind of book.) This fear is absent from the series. Probably because he can't, you know, actually drown (though the few encounters he has had with water lead to him sinking abruptly to the bottom due to his heavy weight, and having to spend several weeks draining out his servos.)
Stephen Dedalus in Joyce's Ulysses is mentioned to be a hydrophobe, although this is probably symbolic of his antipathy toward baptism/Catholicism.
Jayfeather from Warrior Cats is afraid of water. However, he manages to get over it in Night Whispers.
Malcom Reed from Star Trek: Enterprise has a fear of drowning that prevented him from carrying on his family's naval tradition. Oddly enough, this fear doesn't extend to the vacuum of space. Maybe he realized that Space is NOT an ocean.
George Ikaruga from Ultraman Mebius isn't afraid of water per se (he's a good swimmer, in fact). He's specifically afraid of the Ocean. Perhaps justified in his case, as when he was younger, something horrible would happen to him every time he went there. He eventually decided the Ocean just had it in for him.
Hewkii from Bionicle. Other Po-Matoran and Le-Matoran are also shown to dislike water, although they don't seem to outright fear it like he did.
Lesley Lopicana in Mitsumete Knight, a Spiritual Successor of Tokimeki Memorial. She's an Expy of Ayako, but unlike her where the origins of her fear were never explained, we get to know how Lesley got this fear of water (long short story - that you can read in the game's Character Sheet, - it's due to a Childhood Trauma).
Carol Burke, Allen Birkman, and Sierra Manning of Survival of the Fittest v4 all suffer from aquaphobia. In Carol's and Allen's cases, they actually first woke up on the island near the beach, causing them to freak out.
In one episode of The Adventures of Super Mario Bros. 3, Mario become afraid of water after nearly drowning when he turned into a block of cement. But he overcomes it to save his friends and the underwater city.
Looney Tunes character The Tasmanian Devil, namely in his series Taz Mania. "Taz hate water! Taz hate water!"
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.
Sandor Clegane, a.k.a. the Hound, in A Song of Ice and Fire. Quite a reasonable fear, as half of his face has been burned as a child by his evil older brother. He lives in a world with Greek Fire and priests of a fire-god who can, well, magically create fire, and naturally runs into both.
Harry Dresden of The Dresden Files, after his left hand is burned beyond use in Blood Rites, becomes reluctant to even attempt fire magic at all. He eventually overcomes his fears and concerns by the end of Dead Beat, though a villain in White Night mistakenly assumes he's still very afraid of fire and makes a failed assassination attempt based on that.
Torak from the Belgariad was terrified of fire. Kind of odd for a God to be terrified of anything unless one can see the future, as he can, and knows what's going to happen to him.
Throughout his appearances in the Discworld novels, Mr. Slant the (zombie) lawyer is almost completely fearless, even when dealing with sociopathic criminals. As a result of being a well-preserved (and by necessity, extremely dry) corpse however, he is terrified by fire.
In The Wonderful Wizard of Oz the Scarecrow reveals to Dorothy that a "lighted match" is the only thing he's afraid of. Although, given that he's made of straw, can you really blame him? In the movie, the Wicked Witch of the West exploits this fear on several occasions.
Wicked Witch of the West: How about a little fire, Scarecrow?
The dragon in Loom is afraid of fire, a fact Bobbin uses against her with either the Terror or Sleep draft to set her hoard — transformed by him from gold into straw — ablaze.
It's hinted that Milla Vodello of Psychonauts is a pyrophobe due to the orphanage where she worked burning down with the children inside it.
Heather in Silent Hill 3 is afraid of fire. She comments that "it's scary somehow..."
At the height of the Napster controversy, the folks at Camp Chaos created a series of flash animations featuring Metallica's Lars Ulrich and James Hetfield. James, aside from being a caveman mentally, was also terrified of fire. So naturally, in their Celebrity "Who Wants To Be A Millionaire" parody, he gets lit on fire.
Probably alluding to the fact that Hetfield was badly burned by stage pyrotechnics during Metallica's 1992 tour with Guns N' Roses, thus proving that no matter how much they called Metallica a bunch of dicks, their detractors could still out-dick them rather easily.
He's made of wax. In fact, at one point in the film he's in severe danger of being melted because of somebody sticking a burning torch in his face.
Shere Khan from The Jungle Book. At the end of the film, Mowgli chases him away by burning off his tail. Unfortunately, it's revealed in the sequel that burning off Khan's tail actually made him even angrier...
Transformers Armada: Hot Shot, who was forced to leave a friend behind in a fire because he'd passed out from the heat.
Other Things in Nature
Anime & Manga
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.
Films — Live Action
During filming of The Lord of the Rings, Sean Bean was terrified of taking a helicopter to a filming location in the mountains. Enough that he took what to most people would be the far scarier option of climbing the mountain in full costume.
When MythBusters looked at ways flu/cold virii could be spread, Kari Byron confessed to being something of a germophobe. She was the only one not to get "tagged" with Adam's fluorescent fake snot thanks to her previously developed skills at staying away from the ickies.
Simon Tam of Firefly is a cosmophobe (afraid of space), as first shown in the episode "Bushwacked."
A.J. from The River has speluncaphobia, the fear of caves, thanks to having been in a mining accident.
One of the player characters, Rikku from Final Fantasy X has a phobia of lightning (astraphobia), which she gets over in the sequel.
Earthquakes (seismophobia) — Miles Edgeworth from Phoenix Wright: Ace Attorney. The first major crack we see in Edgeworth's stoic facade is that he turns into an absolute mess at the slightest of tremors. It's no better in Trials and Tribulations, when he passes out after an earthquake hits Hazakurain. It also extends to airplane turbulence (which can resemble tremors) and elevators. Justified in it being the result of a traumatic and tragic incident he experienced as a kid.
Jonathan Ingram in Policenauts is a cosmophobe by his own admission, and also appears to show some level of claustrophobia. This clearly doesn't work in his favour when he has to leave the Moon via a material transport relay. Depending on the players' responses to Ed, and how long it takes the player to make the decision to leave, it will extend the action sequence. The first time you beg Jonathan to enter the pod, he will refuse.
The titular monster from It by Stephen King takes on the appearance of whatever its victims fear. One of IT's most well-known forms is that of a Monster Clown, though this image is not always immediately recognized as evil, and has been used to lure in young children. The clown in question is said to smell of boiled peanuts, cotton candy, animal dung, and rotting dead things.
Modern Family: kind of a subversion. Phil thinks his fear of clowns is irrational by nature and has nothing to do with that time he found a dead clown in a field when he was a kid.
Alan Shore in Boston Legal, as we learn when he has a case involving a professional clown who shows up to court in full costume. Alan avoids looking directly at the man for fear of publicly wetting himself.
Supernatural's Sam Winchester remains freaked out by clowns even after years of fighting nearly every supernatural creature imaginable and a visit to Hell. According to his brother, he gets scared when seeing Ronald McDonald on TV.
Zak Bagans from Ghost Adventures isn't fond of clowns. He briefly goes to a place that's right out of a coulrophobic's worst nightmare during the revisit to Goldfield, Nevada: a clown motel. Even the clerk at said motel doesn't like clowns.
In Haven, Audrey Parker and her counterpart, Audrey II, are terrified of a Monster Clown that nearly scared them to death when they were 6.
Barry Dejay in Backyard Sports. He plays worse on the Bling-Bling Brothers Circus in Backyard Basketball just because he is afraid of clowns.
The players of City of Heroes often ask for a Clowns powerset for the Mastermind (pet summing class based on minion-commanding villains), but are denied because Matt "Positron" Miller, the lead developer, is afraid of clowns.
Nathan Drake from the Uncharted series. At the end of Uncharted 2: Among Thieves, Elena asks him on a scale of 1 to 10 how scared he was that she would die, he gives it a 3 or 4. Guess what was at 10?
Likewise, in ''Big Boogey Adventure, Billy's given a spider clown mailman as a hybridization of all his fears courtesy of Horror's Hand. Since Billy must battle his own demons before touching the Hand, Mandy's laser rifle has no effect on said aberration.
Tino from The Weekenders had been afraid of clowns for a long time and just so happened to face his fear the week that... 1. The Carnival was in town 2. The pizza place had a clown theme and 3. There were a bunch of clowns around.
"Mutant clowns from the Hollow Earth! They're real!! WAAAAAAAAAAAAAAAHHH!!!
Velma Dinkley in Whats New Scooby Doo at least. A Monster Clown showing up caused her to swap personalities with Shaggy (who was concentrating on winning a mini golf contest so he went all Velma-esque). They reverted eventually.
Chuckie from Rugrats, although they come second to "the guy on the oatmeal box."
One episode reveals that Didi is also afraid of clowns as she screams at one to get away from her at a carnival.
Caillou's sister Rosie on Caillou, but Caillou helps her to get over it.
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.
Haine from DOGS- the only girl he can stand to touch him is Cute Mute Nill.
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.
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.
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.
Films — Animated
Donkey in Shrek. He has no problem with his best friend being an ogre, and handles the fire breathing dragon quite well, but when Shrek gets an arrow to the butt and Donkey sees blood, he faints.
Films — Live Action
In the film The Darwin Awards, this is the reason why Joseph Fiennes's character gets demoted from his job as a detective.
In William Castle's The Tingler, the theater owner's mute wife is seen to have an intense fear of blood when Vincent Price cuts his hand on a broken cup - this is exploited later in the movie.
Chuckie's dad Chaz from Rugrats faints upon seeing Tommy cut his finger open after the usually brave toddler rescues a baby bird from being squished by a jogger.
The Simpsons: One of Doctor Nick's many undoctorlike traits.
Peter from Family Guy might be implied to be this in two instances, both cutaways. The first is in "Padre de Familia", where he, as a nanny, accidentally crushes two cute children he was supposed to babysit. His response? He vomits all over their bloody corpses, puts them under their bed, and exits through the window in tears. The other is in "Peter's Daughter", where Peter, who becomes overprotective of Meg after she nearly drowns in a flood, breaks down crying from repeatedly smashing Connie D'Mico's face into the fire extinguisher case after she insults Meg.
Anime & Manga
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.
Anime & Manga
Having a character who's very scared of ghosts and anything supernatural is often a Running Gag in anime. Double the fun if the chara's otherwise unflappable.
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.
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.
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.
Skuld from Ah! My Goddess is afraid of ghosts, which is surprising (and funny) considering that she's a goddess.
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.
Naked Snake is terrified of anything involving the undead. Bats make him think of Dracula, and merely mentioning Dracula is enough to give him nightmares. Because Hideo Kojima loves to screw with his own character's minds, Naked Snake gets to face the ghosts of every person he's ever killed in the game. It's a little unsettling for us, the players, but it's horrific for him.
And in the sequel, Peace Walker, we get more ghosts in some bonus levels. When Chico, a fan of cryptozoology, starts describing an optional boss as an "undead dinosaur" brought back to life by Haitian zombie-makers, Snake's phobias kick right back in and he starts trying to rationalize it as just an "ordinary" dinosaur that happens to be skeletal and immune to conventional weapons.
Ragna the Bloodedge's Joke Ending in BlazBlue: Continuum Shift reveals that he is terrified of ghosts. So his joke ending turns him and most of the cast into ghosts. It's canon too; he is freaked out by Sena, one of the personalities that make up Platinum the Trinity, when Sena threatens to haunt him for the rest of his life in an attempt to mooch a meal off of Ragna. To top it all off, the true form of the Big Bad Terumi is a creepy grinning green ghost.
Princess Pitts in Chibi Robo possesses a lady-like terror of monsters and the like. As Chibi-Robo, you can use a Ghost suit to help train her to overcome her fear, though it takes a while and she faints a couple times initially.
Judging from what she says about the Old Chateau (a place where Ghost Pokemon and actual ghosts lurk), Gardenia, the Eterna City Gym Leader from Pokemon Diamond And Pearl has this phobia. (Oddly enough, if you challenge her with actual Ghost Pokemon on your team, it doesn't make any difference.)
Of course, seeing as there are a lot of attacks associated with Ghost Pokemon that are associated with fear and darkness (like Nightmare and Dream Eater, to name only two), and the Poke Dex entries for them tend to make some rather unpleasant claims (which even if untrue, would give them a bad reputation) you can hardly blame anyone for being afraid of them.
In Inspector Gadget, similar to the Scooby-Doo "Velma too afraid of clowns to solve the case" example above, Penny and Brain are at first too afraid of ghosts to investigate MAD's base (and keep Gadget out of trouble) in "The Haunted Castle. Gadget, who doesn't share this fear, is actually pretty competent (proving he's not alwaysToo Dumb to Live) throughout the whole episode — though, thanks to Gadget actually showing good parenting for once (part of that whole aforementioned "competence" bit), Penny quickly gets over her fear, and does her usual investigations herself. Still, the episode somewhat breaks type by having both Penny and Gadget solving the case.
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).
Toni, the punk-loving sister of 1982 Alone in the Dark's protagonist is revealed to be afraid of the dark. It is also hinted to be so strong that it forced her to go to a mental institution in the past.
Sandry from Tamora Pierce's Circle of Magic series is afraid of the dark and always sleeps with a nightlight after being locked in a storeroom. She has a panic attack in the first book when she and her friends are trapped underground during an earthquake.
Criminal Minds: Spencer Reid claims to be afraid of the dark "because of the inherent absence of light."
Doctor Who: But it's not the dark, it's Vashta Nerada. These are microscopic creatures that tend to disguise themselves as shadows. Once you get too near them, you'll be killed instantly. The Doctor tells that these creatures are the reason so many races fear the dark.
Alan Wake: Alice has a crippling fear of the dark. And don't tell me you didn't flip on a few lights yourself after/while playing through the game.
Daniel from Amnesia The Dark Descent has a bad fear of the dark after an incident from his childhood. Staying in the dark too long makes his sanity lower and causes hallucinations, blurred vision, and teeth grinding. Too bad they didn't have very good lighting in 1839.
Chuckie: This isn't just regular-plain-old scary, Tommy. This is THE DARK!
Toph from Avatar The Last Airbender was born stone blind so she only has theoretical knowledge of what darkness and/or it's absence even is. However her tremorsense is rendered useless when she is not in contact with earth, stone, or metal (as well as if the soles of her feet are covered or damaged) and she does not like such situations at all.
Sufferers of PTSD will often have generalized anxiety, including ligyrophobia, the fear of loud noises.
Anime & Manga
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.
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.
Truth in Television on both fears, as a lot of Japanese were still a bit creeped out of said Western inventions at the time, even with Japanese-trained photographers in regards to cameras.
Miyuki Takara of Lucky Star really hates dentists.
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.
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.
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.
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.
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.
In A Certain Magical Index, Hyouka Kazakiri is terrified of Touma Kamijo, despite him being one of the nicest guys on that 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.
As mentioned above, Sakaki from Azumanga Daioh is scared of horseflies, but also of thunder, earthquakes, and even the mechanical guards at construction sites.
Lucy from Peanuts, in her role as a nickel psychiatrist, once diagnosed Charlie Brown as having pantophobia, "the fear of everything". He fervently agreed. This gag was repeated in A Charlie Brown Christmas.
Zatanna has a phobia regarding puppets. It turns out, there is a very good reason for this phobia.
In My Little Pony: Friendship Is Magic Fanfic Progress, Princess Luna ends up mortified of baseballs after getting hit in the face by every last foul ball in a baseball game due to a spell gone hilariously wrong. Some time later, she watched Cupcakesnote An infamous Dark Fic about Pinkie Pie brutally torturing, murdering and baking Rainbow Dash on tv, and becomes terrified of all things pink as well. Though she manages to get over that one in time to hang with Pinkie Pie later.
Similar to the above, Delilah from The Legend of Spyro: A New Dawn is deathly afraid of cupcakes after the "Cupcakes Incident", which apparently involved a run in with the Cupcakes version of Pinkie Pie (Delilah is a Dimensional Traveller). Though it doesn't come up in that fanfic, since cupcakes don't exist in the universe it takes place in, a letter she gets from Pinkie Pie (the real one, who she's best friends with) tells her to call ahead before she visits so her friends won't have them at a surprise party due to her phobia.
Rarity's character arc in the Pony POV Series involves getting over the phobia of gems she'd gotten from Discord's Mind Rape of her. Many other ponies throughout Equestria got similar phobias as a result of their own Mind Rapes, including Prince Blueblood being terrified of the sun, Big Macintosh is terrified of the family dog, Sweetie Belle is scared of her dolls, etc.
The One and OnlyTrixie is revealed to have a crippling fear of Ursas after the Ursa Minor incident in Ponyville. This, rather embarrassingly, rears its head when they encounter two cute, teddybear-sized ones who'd be "fixed" by Princess Gaia's Reality Warping. It scares her so badly that it takes Pinkie Pie singing her a rendition of "Giggle At The Ghosties" to calm her down. Understandably, the others don't laugh or mock her about it, as they know and understand why it scares her so badly.
In Renegade, Shepard has a specific fear of the alien Scrin, and for good reason: she's the sole survivor of the Scrin assault on Akuze, and got an up-close and personal encounter with Buzzers that left her horribly scarred. When the Scrin attack the GDI Embassy on the Citadel, her reaction to close-quarters combat is to go from her normally controlled and unflappable demeanor to shouting and screaming at them.
In Australian horror film Primal, one of the protagonists is revealed to be claustrophobic early in the film, when her friends find a tunnel through a mountain to the other side, where they're headed to see some ancient cave paintings. She has to drive the long way around after she gets a panic attack from entering. Later, the tunnel becomes the only viable way to escape the monsters, as the car's wheels are destroyed and the monsters won't go near the tunnel.
Sid Phillips, the main villain of Toy Story, actually gained a fear of toys at the end of the film as a result of a particular cowboy doll coming to life right in front of him.
Buddy in the first Air Bud is subtly but strongly implied to be fearful of newspapers and loud thumps (often making it a point to retrieve the newspapers and bury them in the former and barking loudly during a court room when the Judge used his mallet regarding the latter). Considering the fact that he was exposed to them frequently by his former, extremely abusive owner, his fear is perfectly justified.
Fear itself (phobiaphobia) — Harry Potter seems to have it... well, sort of. (Well, to be specific, boggarts look like Dementors to him, and Dementors are living embodiments of fear.)
Going by the shape boggarts take, Hermione is afraid of flunking her classes (or maybe failure in general). She was so terrified of this, she wasn't able to use the Riddikulus spell to fight it.
Another example, Professor Lupin is afraid of the full moon. Justified because he's a werewolf.
The protagonist of Iain Banks' Use of Weapons has an odd phobia of chairs. It makes a lot of sense when you learn what the original chair was made of.
Throughout the Discworld series, Rincewind has developed a violent fear of many things, some justified (the Things of the Dungeon Dimensions), some not (having good things happen to him, because it usually means something worse is coming along later), but the thing he seems to dread the most is plots, because if a plot starts happening anywhere near him, eventually he will get sucked into it. Rincewind was afraid of playing football in Unseen Academicals, but then so was every other wizard except Ridcully.
The short story Echoes of the Tomb details his first encounter with the Necrons, they slaughtered everyone else on the tomb complex and took off two of his fingers as someone took a fatal shot for him, he only survived by jumping through a warp portal that happened to lead to a Necron ship boarded by Space Marines.
Several characters in Dean Koontz's False Memory have phobias. Susan Jagger is agoraphobic and fears leaving her house. Martie Rhodes is autophobic, meaning she's afraid of herself (specifically she's afraid that she might commit a violent act). And the nameless wife of an Internet billionaire is terribly afraid of Keanu Reeves; she can't look at pictures of him and can't watch television because she might see a commercial for one of his movies.
The closest to karmic retributionThe Talented Mister Ripley receives is that he develops a fear of cops for the rest of his life. He can never look at another cop again without a brief flash of alarm as he thinks that the cop has discovered his crimes.
Dan Brown's Robert Langdon is severely claustrophobic as a result of almost drowning in a well as a child. He regularly has to enter confined spaces in the novels, including being imprisoned in a coffin in Angels and Demons and actually faces drowning in tiny space in The Lost Symbol it turns out to be a total liquid ventilation system, but he didn't know that.
Adventure Hunters: Lisa is terrified of gargoyles because of a bad encounter with them in her childhood.
Noise — Leonard Hatred in Look Around You, invented "Psilence", a type of liquid skin that blocks the ears, as a response to being subjected to loud noises all his life. (Unfortunately the mental instability caused by his condition ultimately led him to attack Sir Prince Charles at an award ceremony.)
Tommy from Big Wolf on Campus is afraid of ending up alone due to people finding out about his lycanthropy. And Merton is scared of monster movies (which is kind of weird, because he's a Goth).
Balloons (globophobia) — Lacey and Davis in an episode of Corner Gas. Also, by the end of that episode we find out that Brent seems to have a fear of globes.
Wanda's implied agoraphobia (fear of open space). It's especially ironic as she lives in Saskatchewan, which has nothing but open space.
As revealed on Attack of the Show!, co-host Olivia Munn is also afraid of balloons. Needless to say, fellow co-host Kevin Pereira takes so much delight in tormenting her whenever the subject comes up.
Embarrassment: Richard Hammond. "I have several recurring nightmares. One in which I am presenting a radio show and can't work the desk, another in which I find myself on stage with a truly catastrophic band. I am only waiting now for Top Gear to make me run naked through a shopping centre on a Saturday and I will have completed the set."
Alan Statham from Green Wing is scared of goblins. When Joanna decides to scare him (because his cheerfulness was annoying her) she asks her dwarf cousin to hide under his desk, with green make-up over his face and jump out at him shouting "boo!". Statham then beats him to death with a heron.
Porcelain (porcophobia?) — Guybrush Threepwood. Speculated to have been caused by being hit over the head with a porcelain vase in the first game.
The developers have said they added this just as a gag. After all, who is scared of porcelain?
Referenced in Tales Of Monkey Island Episode 1: Launch Of The Screaming Narwhal, when you have to pick up a porcelain action figure. Guybrush grits his teeth and reassures himself "Calm down, Guybrush, it's only a little porcelain..."
AGAIN Emma Emmerich shows up on this list: she doesn't like sea lice at all.
And we also have Big Boss himself, scared of vampires and zombies. This is a subversion in terms of the 'recurring obstacle' trope - vampires are in the series (in aform, anyway), but Big Boss never encounters one.
Bald people: May of Guilty Gear has an extreme fear of bald men, and can even sense when someone is bald, as shown during the Story Mode in XX when she runs into Dr. Faust (who, under the paper bag, is bald).
Battler Ushiromiya is terrified of any vehicle that shakes when it moves, as was his late mother Asumu.
Flora, Layton's ward in the Professor Layton games, is afraid of being left alone (monophobia).
Artix, normally fearless paladin extraordinaire in Adventure Quest Worlds, is utterly terrified of the color pink (which Beleen mercilessly teases him about).
All dwarves in Dragon Age (apart from those born on the surface, obviously) tend to have some fear of the sky (possibly Agrophobia?) due to the vast majority of them living in underground cities. They fear that going to the surface will not only make them lose their 'stone sense', but that they will fall up into the sky. Of the three dwarves you can recruit, one is a surfacer anyway, and the other two overcome their discomfort fairly quickly. Anders the mage appears to have claustrophobia, given his comments whenever you venture to the Deep Roads in the Awakening expansion (and in Dragon Age 2). There are also plenty of people who are terrified of mages/magic/demons, and of those, plenty are justified.
In Ib, Garry is utterly freaked out by all the blue dolls. Can't blame him considering one of them stalked him down a hallway and there was another time where a whole bunch of them captured him and forced him to play a game with them, but he found them disturbing even before any of them did anything.
Bob of Bob and George is spectacularly phobic of Pokémon. For no adequately explained reason. We'll state this again: a character with fire superpowers who intermittently seeks to conquer anything he doesn't destroy is terrified of Rattata.
Hats: Trel from Cwens Quest has either violent fits of terror or near psychotic reactions to hats due to childhood trauma.
Xenophobia: Insecticomics Dreadmoon. Due to the humorous nature of the comic it's more a strong disgust than outright fear; in Wayward's more serious fanfiction he's uncomfortable around non-Cybertronians and outright terrified of organics.
Katia of Prequel is deathly scared of nobility, including having a nightmare of Uriel Septim as a Humanoid Abomination (while in-universe he's the Big Good) and being rendered speechless at the sight of Martin Septim (at that time merely a priest in Kvatch).
Mandy from The Grim Adventures Of Billy And Mandy is afraid of professional figure skaters (although she insists she just "doesn't trust the way they spin"). Billy confronts her on this fact when she says his fear of clowns (see above) is stupid. (And frankly, he kinda has a point...)
Horror's Hand in Big Boogey Adventure conjures up something worse for her: a future Mandy that is obese, mirthful, and married to Irwin. Mandy is scared shitless.
In Transformers Prime, all the robots, but particularly Bulkhead, are afraid of scraplets, whipping out their weapons at the sight of one. But considering they're essentially the robot equivalent of flying piranha, it's not an irrational fear.
In an episode of Popples, Billy says he is afraid of the dentist.
In addition to clowns, Timmy Turner is creeped out by barefeet. Which he may have developed from rubbing his grandma's feet.
Vendetta from Making Fiends has a hatred of music (melophobia). There's a big zig-zag in how extreme it is; she hates Charlotte's singing, but sometimes she will sing herself (and very badly). In the last three episodes of the web series, she seems to be traumatized by music playing from a card, firing her assistant Grudge because it keeps playing when he burps. When her new assistant Rubella gives her a musical bear, Vendetta falls to the ground writhing in pain. In the TV series, she seems to hate music mostly because it's happy and she hates happy things.
Sterling Archer has three great fears. Two of them are alligators and crocodiles. The third? Brain aneurysms, because they strike anywhere, without warning.
Hitchcock also had a lifelong fear of policemen (dating from a childhood Scare 'Em Straight incident), which is why so many of his protagonists end up wrongly accused.
Interestingly, Joey from Full House mentions eggs as one of the things people tend to fear.
In a magazine from years ago, Hilary Duff stating her fear (or strong disgust) of eggs.
Stephen King is afraid of the number 13, a condition known as triskaidekaphobia.
Composer Arnold Schönberg similarly was afraid of the number. His greatest fear was reportedly dying on an age whose digits added up or multiplied to 13. Which he did, at age 76 (7+6=13) on Friday the 13th - perhaps because he feared it that much.
French composer Jules Massenet shared their fear as well. Made weirder and arguably funnier by how the letters in his name are... thirteen.
Pamela Anderson probably has the above beaten. She is reportedly a sufferer of eisoptrophobia — in other words, she is freaked out by her own reflection.