5/8 MDF vs 3/4 MDF
 

What is the difference in a sub box when made from 5/8 MDF or 3/4 MDF?

depends on the subwoofer and how large the box is. for 8" subs you can easily get away with 5/8" MDF for anything bigger I'd really reccomend 3/4" the enclosure will resonate less and be a fair bit stronger. If you're going fo a monster sub setup with lot of power 1" MDF with a lot of brcing is the way to go.