Depends on the situation.
HDR - Pro HDR. If you find Pro HDR too slow, use HDR Photo Camera (set in bracketing mode, with Low Loght bracketing on) to take the photos, then process them later in Pro HDR.
Low Light - NightCap for quality, SlowShutter for ease of use (though quality suffers in this app). 645 Pro technically has the best quality night shots available, but NightCap allows for manual shutter speed control, and easier focusing.
Normal - 645 Pro has the best quality available, especially when in TIFF output mode, though I sometimes use HDR Photo Camera anyway, as it takes three photos at different exposures extremely quickly.
That being said, the normal camera app works fine for most people in most situations, just don't expect the world.