Both times I've taken the MNFF quiz (I sampled the new quiz they are making), I was Sorted as a Gryffindor. I try to answer it truthfully, but some of the questions really depend on what you feel in that spur of the moment. Obviously, the quiz can't see inside your head as the Hat can, so it's definitely not going to be as accurate. The questions I think look into the outside layer of your personality, and Sort you by that--whilst the Hat probably looks at your mind in its entirety, and figures out your priorities.
On a personal note, whilst I do think I'm a Puff through and through, I doubt the Sorting Quiz on MNFF is a true evaluator of our abilities. Does anyone really answer it truthfully?