Clock: Being forgotten - His teammates forget about him the moment they enter his head, they spend the episode trying to remember what they need to do
Snowball: Being armless/weak - Snowball doesn't have arms, TSTOE has to get through to him while he keeps getting more and more reckless trying to prove that he isn't weak
Donut: He doesn't have a canon fear, but I like to think the time he was factored with Four affected him more than he likes to admit - Donut gets factored with Four again and gradually loses control over their powers, his team either has to help him get control or to somehow remove Four from his body
Golfball: Having no control - She doesn't usually have control over everything anyway, but she'd probably really hate having no control at all, maybe put her in cage and have her unable to do anything while her team has to free her