Commander Badass from Manly Guys Doing Manly Things hates millipedes. This comes from doing a term of duty on the millipede planet in millipede season where everything was covered, filled with, or spawning millipedes. Which really sucks because his daughter has a pet millipede.
O-Chul from The Order of the Stick may or may not be afraid of sharks (galeophobia) after events in the comic, but he says the line of the trope almost verbatim. Though considering that Xykon continually had O-Chul tossed to sharks of varying nonsensical breeds during his imprisonment in the conquered Azure City...
O-Chul: Sharks. Why did it have to be sharks.
Isabel from Paranatural is afraid of dogs due to an incident when she was younger.
Trees (dendrophobia) — Durkon from The Order of the Stick. This seems to be a racial thing, with Thor-worshipping dwarves being convinced that their god smites tall trees for being wicked.
In Scandinavia and the World, Denmark is afraid of nature itself, everything from butterflies to waterfalls. Curiously enough, he's just fine with domestic animals. And the sea, to the surprise of Norway and Sweden here.
Thog from The Order of the Stick is defeated by an illusion of a female orc. Haley takes offense that his fear of "pretty girls" doesn't seem to extend to those of other species.
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 Cwen's 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.
Varden of Inverloch is petrified of magic and goes all sweaty and bug-eyed whenever he sees it (or when it's used on him). Neirenn, the group mage, takes advantage of this whenever they're arguing over something.
Quintin from Jupiter-Men is terrified of doctors, nurses, and hospitals and would rather see anything else. Even when he's freaking out over his powers turning him into green slime and sticking him to everything, he'd much rather revisit the site of the explosion for clues than see a doctor. He's so desperate to avoid seeing a doctor that he offers to buy Jackie whatever clothes she wants to get her to agree with his plan to visit the construction site.
Pebble from Pebble and Wren is afraid of being alone and toilets (the latter because he thinks they're alive).
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).
PeeJee in Something*Positive has been shown to have an almost pathological fear of puppets.
In Squid Row, Randie is deathly afraid of garden gnomes.
Connie of Waterworks is germophobic, and tends to freak out around toilets.
Gray from Weak Hero has an intense fear of rooftops ever since his best friend was pushed off one and hospitalised. When Ben discovers this, he relocates the gang's hangout spot from the rooftop to an empty schoolroom. Then Wolf demands that Gray be taken to a rooftop for a fight; this is how Gray suffers his first serious beating in the series, as he's too afraid of being on the roof to retaliate. Not at first, anyway.