Some more reading around here on HN and checking on other people's recommendations has led me to this:

http://lifehacker.com/software/feature/practicing-simplified...

This actually matches pretty closely what I started with. My system has evolved a little further, and it seems I deal with more paper, but this is a better summary than I otherwise might write.

These are linked to and form a crucial part of it:

http://lifehacker.com/software/geek-to-live/the-art-of-the-d...

http://lifehacker.com/software/top/geek-to-live--empty-your-...

The email advice is especially important to me. I do file things into reference folders, but I have scripts to do the donkey work on that.