Given that I've suffered from panic disorder for 12 years, there are a lot of run-of-the-mill things that have shat me up over that period.
However, some longer-standing fears would include being in deep water (swimming, canoeing) and one that I've had for as long as I can remember is being terrified of falling into the water between a ship and its dock.
I'm also prone to bad fear when in a situation over which I have no influence or one where I'm completely reliant on something else. So, flying is bad because, short of committing an arrestable offence, I'm stuck on the plane until the time when it's scheduled to land. The prospect of fiery plummeting death doesn't bother me, it's being unable to get out that I don't like. If I decide I don't like it halfway through the flight, that's tough. Bus or train? Fine. If a freakdown is approaching, I can just hop off at the next stop.
A good example of this was taking the cable car to the top of the Aiguille Du Midi in 2001. Within seconds of getting out the cable car, I watched a tandem parapont go wrong when the canopy didn't open on takeoff, and the two guys started sliding down a convex slope which ultimately became a couple of thousand foot drop. I seemed to be the only person that noticed this whilst it was happening. They did manage to stop themselves, although beyond the point where they could walk back to safety, and they were eventually choppered off. However, the fear kicked in at the notion that I was really rather high up, walking off the hill wasn't a realistic option, and getting down depended entirely on the cable car. Poo was almost flowing freely from me by that point.