I've worked from home for 20 years, and came back a couple weeks ago from a conference where one of the sessions I attended focused on organizing your home based business. Whatever area you are using to work from, the first thing to do is REMOVE EVERYTHING from that area and put back first only your essentials (desk, chair, computer, etc.) Then one by one decide what is crucial and what can be located in another area (i.e. things that only need to be accessed occasionally, like archived files, reference material, etc.)
Make sure your office is located (if you can) in an area that's not "grand central" in your home. Also make sure it's light, bright and conducive to productivity. Figure out an organization system (that works best for you, not everyone works the same way) and get everything in order so you are on the right track from day 1.
I came home from this conference on a Saturday evening and spent the entire next day doing just this, and what a world of difference it's made for me!