Make sure your case fans blow inward. This way, all random holes in the case, from the ones intended to be there to random gaps will have air blowing out of them, which means that they can't suck in dust. That way, you know which holes are sucking in air -- the ones with fans on them -- and you can put filters on them. Of course, this also requires that you check the filters from time to time, and probably clean or replace them, too.

Alternately, if you have a case that's designed to have an in-fan and an out-fan, see if you can make the in-fan blow harder than the out-fan sucks. Basically, you want to make sure you have positive pressure inside the case.