If I remember correctely, basic GTD says to do something like this:
--> Do you need to do anything with/for it? Put it in the related action context folder. I personally use just one folder called "Action Support"
--> Is it project support material? Put it in the appropriate project support folder.
--> Do you need to think on it a bit? Put it in the tickler file
--> Is it pure reference? Put it in the appropriate reference folder. (Which letter you file under is up to you -- client name, project name, etc.)
I don't get much hard copy paperwork, so my stuff is organized on the computer. I used to use GoldMine but have been using Time Matters for the past few weeks and I like that a lot. I can simply open a project and click the Docs tab to see paperwork, web tab for related sites, email tab for email, billing tab, etc. And I can see at a glance if there are next actions scheduled, and where I am in the progress of things. Same applies to just contacts (without active projects).
Hope that helps,