Well, if you're going to do it, MDF makes sense to me as it's what the sub is made of as well. That's just my 2 cents.
BTW, I had a similar idea and when I built my equipment rack I made a cabinet at the bottom to hold my sub. Unfortunately as soon as I put the sub in there and listened it was very 'boomy'. So I pulled it out and did the sub crawl and have been happy since. Luckily for me the sub crawl revealed I could put the sub in an optimal and aesthetically pleasing place. The ex sub enclosure now holds movies, games and my PS3 controller charger.
