I'm re-organising my room to make it most productive for my work (which includes some coding). A while back I saw a really interesting section on the Guardian website featuring pictures and descriptions of famous authors' rooms (http://www.guardian.co.uk/books/series/writersrooms). So I thought it would be cool to find out what hackers rooms look like.
What does your room look like?
Step 1: Empty desk. No cups or paper holders or anything like that
Step 2: Digitalise what can be digitalised, and sort away all papers that are not directly relevant
Step 3: Get 2 baskets, one for unimportant papers, another for papers you have to order. When anything comes in that is not critical, drop them in the basket. Don't keep the basket on your desk, keep it away in your cupboard. We don't push paper that often.
Step 4: Sort the cables out. Tape them, put them away sensibly
Step 6: Get really good lights
Step 7: Get something to play with for when you are thinking. I personally use a 50 cm wooden ruler, and apart from my PC and a pen, that's the only thing on my desk. If I did not have it, I'd have chewed the pen dead by now.
When you work with a clean desk things feel a lot tidier. When you have stuff on the desk, only when they are extremly high priority. Having a neat desk will make you focus even better on the stuff that is important when it does come on your desk.
And if you have a desktop, consider moving it somewhere else. I keep mine in the closet and use it via network - that way I have some quiet.
So, my suggestion is to plan in a way that it gets difficult to get untidy.