I always depress mine all the way to the floor. I've heard varying opinions on this, and it does seem like it varies from car to car. But with my GTO it seems like it gets touchy sometimes when the pedal is just a short distance from the floor if I try to shift it. I figure I'll play it safe and push it to the floor all the time.
I also have short legs, and do feel like my leg is stretched pretty far to get it to go all the way to the floor. This only bugs me though if I'm sitting there holding in the clutch, which doesn't happen too often as I generally idle in neutral.
06 IBM/blue M6 18"