I use manual when I do macro (well, near macro, I dont really have a real macro lens and I dont have any of the other necessary macro equipment), in which case I set the camera to nearest focus point and just move it around instead of using autofocus or touching the manual focus control any further, or when I want to use some really unusual kind of focusing.
Like, I tried to "paint" color recently by setting my lens to nearest possible setting and photographing stuff far away. Turned out I didnt actually liked the result, though. Maybe I need some really wide aperature lens so the background actually turns into mush and doesnt just look out of focus.
Well, just as an example for when I would disable autofocus. In general, I use autofocus all the time.
Ever since I had the D600, I can finally see if things are actually in focus, or not. Not possible with my D5100 before. Thus, on the D5100, I always used autofocus.