There's a great tip on Lifehacker today about using iTunes as an organizational tool. We've all got lots of PDFs sitting around; some important, some not. Instead of burying them in a series of nested folders within your Documents folder, use iTunes.
Make playlists for your different categories (like "Taxes" or "Parenting Committee"), add your files and you're done! Drop the lot into a "PDFs" folder and you've got organized, search-able files in an application you've probably got running anyway.
If you want to take this a step further, follow the full tutorial at Lifehacker and create a PDF-only iTunes library.