Inverted always, because it's insanely more logical. If you picture the imaginary camera floating behind your character (be it his/her/its back or his/her/its eyes), think of the movement you make to have the camera point to the sky. You tilt back on the base of the camera to angle the front upwards. You tilt back your head to look at the clouds. You pull back on the thumbstick, joystick, or mouse. The opposite occurs when angling the camera down. Besides the fact that flight controls respond in the same manner.
Flying or shooting, it doesn't matter. I'm liking how more and more games invert by default, so the "invert" setting actually does that horrible flip-flop where pushing up on the stick makes the camera go up. At least 'round these parts, every time I jump on someone's XBOX to Halo or whatever, it's almost always inverted. The host will point out profiles that aren't inverted because they are weird and counter-intuitive.
Oh. Wargamer just posted the exact same thing. I agree! So much more natural. And JagoGuy's explanation was pretty deep. Interesting thoughts...
Edit: What I want to know is who inverts their x-axis, because I see that option in games, but it scares me. Who wants pushing right on the stick turn their avatar left!? Madness.