S.A.
www.flylady.net has some very helpful suggestion for just your situation. It sounds like you are Born Organized, but he must be taught. Trust me, as one who has had to teach myself (with FlyLady's help, of course) how to be organized, this situation must be just as frustrating for him as it is for you, but he's overwhelmed with the decision making/sorting out, and THEN there's still the actual work to do!
Here's my .02 worth of my experience as a homeschooling mom to a 4th grade girl, and a 1 grade boy, and I take care of an ADD 2nd grade boy several days a week, and help him with his homework: At this point, you probably need to guide him, every day, through organizing his homework order. If he is behind in his homework because of the disorganization, you can ask his teacher if he can still turn it in. This weekend, you can try telling him he needs to work WITH YOU on organizing his desk/papers/whatever for 15 minutes. Set a timer (this is really key). Instead of you doing it for him, you can ask him when this paper is due, and put them in order. Maybe it's possible to get a list of homework, and when it's due, or what he's missing, from his teacher, and walk him through the process with that list in hand. If one 15 minute session isn't enough to tackle this project, give him a break (my 6yo DS needs about 45 minutes to an hour between 15 minute session of a new skill, and my 9yo DD needs about 15 minutes), and tackle it again for 15 minutes at a time 'til it's done. I think the most important thing is to remember that his brain is wired differently than yours, and this may just be a difficult skill for him to learn, and maybe one that came naturally to you. Be patient with him, and break down your own organizational thought process into single-question segments, and let him answer each question aloud to figure out which pile/folder/whatever to put things in.
Also, to minimize school paper clutter, if it's something that he doesn't need for school anymore, use a box/big binder/whatever to keep the stuff HE wants to keep. If you help him go through his graded/returned papers once a week, and he gets to choose 1 to keep each week, then he'll feel some control over the process, and that will help him "own" his work! :)