I have built probably 15 boxes for me and my friends and MDF is the ONLY way to go...
The one's you buy from Best Buy, Circuit City, etc...all fall apart after 1-2 years..
My boxes are sturdy as hell..but as someone mentioned earlier, drill pilot holes and then counter-sink the screws so when you carpet it, you have no bumps..
Also, if you go to Home Depot, they will cut the pieces for you, just have the exact dimensions you want. Then rent a jigsaw and a belt sander to finish the subwoofer hole and sanding it smooth. Maybe $30-$35 total cost..
Greg