What is (are) the accidental cause(s) most feared by the flight crew?
What crews should be most concerned with is indeed crew error.  In the 1930's and 1940's, more accidents were caused by mechanical failures -- things failed that made the airplane unrecoverable.  Several decades ago, crew errors became the larger source of accidents, where a flyable aircraft (albeit with perhaps some issue, but flyable nevertheless) crashed because the crew did something that made the situation worse.  The hardware these days is pretty darned reliable, and if "you" do what you're supposed to do, chances are really excellent that you can get it on the ground safely.

That said, pilot psychology plays a major role in answering the question, since pilots strongly prefer to be "in control."  Or, less formally, we all tend to be control freaks.  (Not necessarily in every area of our lives, but certainly in the cockpit, we tend to have "take charge" personalities.  If something isn't right, we want to make it right, and a laissez faire "eh, whatever" attitude doesn't tend to be found among pilots at work.)

So the things that most concern us at a more visceral level, I'll suggest, tend to be the things that we can NOT control.  If an engine catches fire, I'm confident I can put it out with the procedures and tools that I have, and I can get the aircraft back on the ground because I'm trained to do that even with one less engine than usual.  But if there is a raging fire someplace that I can't control (electrical wires -- SwissAir Flight 111 or cargo hold -- ValueJet Flight 592), then that bothers me.  Similarly, Terry's scenario of cargo loading done wrong -- outside my control, and the pilots have to trust that somebody else did their job correctly.  And by the nature of that being entirely outside my control, that tends to be more of a troubling scenario than any of the typical list of things that I can control and have been trained for: engine fire, depressurization, electrical issues, etc.