RWBY: During the tournament matches, Team SSSN is pitted against Team NDGO. The battle arena is given two sets of terrain, desert and water. While Team NDGO is delighted to have a desert terrain, having come from a desert homeland, Team SSSN has a very problem. Their team member, Neptune, has a crippling fear of water. As soon as he sees the water appear behind him, he races forward and climbs one of the cliffs on Team NDGO's side. Although he claims it's a tactic the opponents would never expect (they admit that's true), it's obvious to the girls why Neptune's doing it. At the end of the match, the girls take up position in the water in the belief that Neptune won't be able to touch them. Unfortunately for them, Neptune's weapon is electricity-based. When he reluctantly gets close enough to dip his trident into the water, it's game over for Team NDGO.
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.
Flying (aviophobia) or Heights (acrophobia)
In Red vs. Blue, one of The Meta's only weaknesses is that he's afraid of heights. His death is appropriately ironic; he's knocked off a cliff into the ocean.