Most of my file organization is done shortly after the stuff comes in, but trying to wield around all of it can get irritating.
The thing I hated was desktop icon clutter, especially since I never used most of them (by comparison, my desktops in Linux are clean since DE standards there tend to repel said clutter naturally), and I don't like the idea of having actual folders on my desktop to store the stuff in. But I found the solution to all that: XLaunchpad
. The few ones I do use often are on the first page, and the other less-frequently-used on the second. And if I need to use my standard Windows desktop, all I have to do is hit F12 and the clutterific one comes right back.