I don't know what kind of work you do, but at my graphic design job every project has a job number. Everything related to that project includes that number: all the proof PDFs (with r1, r2, r3, etc. for revision number 1, 2, 3, etc.). The layouts have that number, too. Plus I put that job number in emails to allow for easier follow-up and tracking.

When jobs are finished, they are archived onto CD (eventually DVD once we run out of CDs). The archive discs are alphabetical by client. So disc D-32 has finished jobs for clients whose name starts with D, and the disc insert has an index written up with what projects are on there, so we can easily find old files, since a lot of times an ad that ran last year may be updated for this year.

I have no idea if this helps any or if it's completely unrelated to what you're doing, but you haven't really explained what kind of jobs you're tracking.

Oh, and if you read GTD closely, you'll notice that prioritizing projects is irrelevant. It's either do it now (or soon) or do it someday-maybe.