There is a worthwhile discussion going on over on whatdoiknow.org with respect to organization and computer file naming conventions.

I accumulate files on my desktop until I lose track of them, then I'll package the related files up into a job folder and move it into a current projects folder. Once the job is done, I'll move it over to our file server for archiving. By that time, (hopefully) we have a reference number which I'll prepend the job folder title with.

We also break the archives down into logical job types. It works for me. Where it gets ugly is with shared folders. Everybody has there own variations, and we also seem to be losing files - even though we save everything.

And, anymore - so much of what I do is in e-mail that that's the first place I think to look for it. I find almost 90% of my work and organization happens within a series of giant .pst files these days.