[JKT]

.oo3 if you have OmniOutliner 3 (is it .ooutliner for earlier? I forget) and .graffle for OmniGraffle will find all files in Spotlight.

You can add comments to the Spotlight field of any file (which can be automated using an Automator action) to allow you to specify unique metadata for searching.

There are probably easier ways to do all this, but I haven't learnt them yet.