For joysticks and controllers, I prefer inverted. My main reason is that as a kid, I played a lot of flight sim games and obviously used a joystick. Planes go up when you pull back and down when you push foward, so I obviously wanted my FPS games to work the same way.
I do, however, use non-inverted for computer FPS's with a mouse. My main reason here being that I have never played a flight sim with a mouse, and as a long standing computer user, moving the mouse up meant moving the cursor, or in this case my point of view, up.
The controller thing gets quite annoying as most people I know use non-inverted. I guess they never played Commanche 2 or X-Wing as kid, huh?