I picked up this tip in this forum somewhere along the line, I think. I have created 5 folders that sit on my desktop:
0. Inbox
1. Actions
2. Review
3. Current Projects
4. Archive
I use the inbox to collect email attachments that come in, etc. From there, I can process/clarify by moving things to either Actions or Review or Current Projects (which is a collection of folders for projects I'm working on now). Archive is an A-Z set of folders - like a big digital filing cabinet.
Periodically all of these folders require purging if I don't stay on top of them, but at least the digital mess is contained in 5 folders
I also use Evernote to store notes and reference items.