i just did long division with DD because she wanted to know how to deal with really big numbers, and while i'm not sure what mechanical issues your DS might have, the plain old pencil and paper was really helpful for us. you could try scribing for him a bit as you talk it through, if that might work?
i don't know if this will be at all helpful since every kid's learning style is so different, but i started by asking DD to think about what the number we were dividing really meant (just verbally expanding it.) then i framed the entire process as simply breaking that big number down into a lot of easy little divisions - and that she could keep on going until she had dealt with the entire number.
we started with one she already knew (64/8), so that she could think about the meaning of place values as she went along, next we added an easy remainder-type problem (42/5), and then all bets were off - suddenly she was flying through stuff into the hundreds and thousands. that shocked me a bit, because from my own experience, i remember thinking long division was an interminable series of finicky steps... i feel pretty lucky that i happened to hit on the right approach for DD!
i'll be eager to hear about apps, too, though. nothing like a digital carrot to get in some practice (which she hates!)
