What exercise can I substitute for box squats on CW's Strength-Focused Mesocycle.
Could you link to the specific cycle you mean? I'm not quite sure what the other exercises being used are, but, OTOH...
Romanian deadlifts with a pause at the bottom
Disregard if these are already used/inaccessable, of course...
Box squats aren't very hard to implement and have a lot of qualities you can't easily duplicate with similar exercises. Chances are they're being used because they're easier to recover from. A box made from plywood framed by 2x4's would be more than strong enough and would only cost you a couple dollars to make.
You can do them off a bench if you dont have a box.