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.
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.
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).
Riff also will end up in Torg's arms if somebody mentions the DMV.
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.
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.