And Fluttershy is shown to be utterly terrified of dragons in "Dragonshy". (Well, huge adult dragons, anyways. Small baby ones, like Spike, apparently have the opposite effect.)
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.
Gene from Bob's Burgers reveals his fear of snakes in "It Snakes a Village". He even sings a song about it.
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?
Billy from The Grim Adventures of Billy & 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 chews 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.
Bubbles is afraid of cockroaches and wasn't happy when she had to eat one while disguised as Boomer.
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.
He's not terribly fond of bugs in the 2003 series either, as seen in April's Artifact
Raphael I ain't scared!I just hate bugs.
Michelangelo What about that huge one crawling up your shell?
Raphael Where?! Where?!
In The Grim Adventures of Billy & Mandy, Billy is deathly afraid of bugs, including spiders. This naturally creates a very awkward situation when Jeff, a Giant Spider who thinks Billy is his father, shows up. (Billy overcomes his fear and reconciles with Jeff in the third full-length movie.)
Mice & Rats (musophobia)
Mammy Two Shoes from the Tom and Jerry shorts, as well as similar characters from various animation.
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.
April O'Neil from TMNT 2012 is terrified of bats. This is because of her father becoming a bat mutant.
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 because of how he was brainwashed by a cat villain back in the first season (and his memories of the incident apparently returned).
Even though they are part of somewhere else, Code Lyoko's Aelita is scared of wolves.
The Grim Adventures of Billy & Mandy: Irwin has a fear of bears. This, combined with the telling of jokes to and audience, is his worst fear as revealed in Big Boogey Adventure. Cue Horror's Hand conjuring it up for him.
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.
Scott from Total Drama is deathly afraid of sharks, which makes sense considering that he had a brush with Death after he got mauled by Fang, thereby scarring him. Even being near Fang is enough to put him in a blank state.
Gretchen in Camp Lakebottom has a phobia about chipmunks, although she is seemingly cured by the events of "Cheeks of Dread".
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.
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!"
In Batman: The Animated Series episode "Torch Song", singer Cassidy developed a fear of fire after her ordeal with her ex-boyfriend-turned-supervillain Firefly.
Lumiere from Beauty and the Beast, despite being turned into a candlestick holder. 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.
In a the second part of a two-part Cliffhanger episode of King of the Hill, Hank was almost killed when Buckley blew up the Megalo Mart after mishandling a propane tank, and he became deathly afraid of propane as a result, a very bad handicap for someone like him who has made a career out of selling it. Fortunately, he managed to get over it.
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.
In SilverHawks, Timestopper is terrified of the dark. In his case, it's because he can only use his time-freezing powers in the light, and he's nothing but a scrawny 14-year-old kid without them.
In Inspector Gadget, similar to the Scooby-Doo "Velma too afraid of clowns to solve the case" example below, 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.
Scootaloo in My Little Pony: Friendship Is Magic confesses to Rainbow Dash that she is afraid of ghost stories but did not want to admit it sooner for fear that she'd make her upset.
Numbuh Three in Codename: Kids Next Door is afraid of the hamster ghosts that show up in Operation: G.H.O.S.T. (after she starts mourning too long over the death of one of the team's power-providing hamsters) but she does think they're cute.
Kinda doubles as an Ironic Fear, as he is a fan of Krusty the Klown.
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. They saw a movie titled Mutant Clowns from the Hollow Earth 2. The Carnival was in town 3. Tino notices the arcade entrance has a clown face 4. The pizza place had a clown theme and 5. There were a bunch of clowns around (because there's a clown convention in town).
"Mutant clowns from the Hollow Earth! They're real!! WAAAAAAAAAAAAAAAHHH!!!"
Velma Dinkley in What's 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.
Mandy from The Grim Adventures of Billy & 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.
Fry appears to have a fear of parade size balloons...until quickly gotten over it by Bender.
In an episode of Popples, Billy says he is afraid of the dentist.
In addition to clowns, Timmy Turner is creeped out by bare feet. 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.
Trina Riffin from Grojband has automatonophobia (the fear of puppets) ever since she was a child.
The last season of Super Friends had an episode where Scarecrow discovers Batman has a fear of Crime Alley. Scarecrow doesn't know why he's afraid of it (it's where Bruce Wayne's parents were murdered), but since he's never seen Batman show fear of anything else before, he's quick to take advantage of it.
In My Gym Partners A Monkey, Principal Pixiefrog is paranoid about lawsuits. (Not surprising, as his school is clearly not up to code.)
In Codename: Kids Next Door, Numbuh Four appears to have hemophobia (fear of blood) in "Operation: SAFETY", freaking out when he thinks his baby brother Joey is bleeding (even though it's just ketchup) and fainting when he sees that he has real blood on his knee.