I think the stacking order, or the position in the filter holder if you are using only one filter, can actually matter, and that depends largely on the aperture you use. If you have, let's say, a graduated neutral density filter with a hard dividing edge, you better use it in third position, farther away from the lens, if you want to keep that well defined edge with a wide open aperture. If you want a softer edge, put it in the closest position... It does make a difference.
And if I'm not mistaken, the polarizer usually goes in first position... please correct me if I got that wrong.

We do not see things as they are. ǝɹɐ ǝʍ sɐ sƃuıɥʇ ǝǝs ǝʍ