I am solving this issue as follows:
Use a good viewer like pdfxchange viewer (close to Acrobat, more than a viewer): Tracker Software Products :: Downloads
So I edit pdf metadata (CTRL+D) and add any keyword I like, comma separated, I think of it as tagging.
Then using its "search pdf" you can specify location (it could be a whole drive) and just uncheck "include pages content" (for lightning speed). It will pick from your keywords as well from other doc infos, as title etc. So by using a keyword you'll pick all tagged files.
I also keep a tag list somewhere (text file, piece of paper..) for convenience.
I have tried using file manager programs, but it turns out they copy tagged files into their program directory, so they duplicate disk space, which is unpleasant to me.
I only found one, Stuff Organizer from sourceforge, where you can avoid this issue by leaving "new directory" as blank field, so it will basically index the source file itself. It's up to you..