I use Evernote as my portable brain, and I use primarily tags for organization. "Inbox" and "Reference" are my two primary folders - anything actionable goes into the inbox, and everything else (manuals, recipes, etc.) goes into the Reference folder. I have a handful of shared folders in use, as well. The thing that finally made it work as a GTD system for me is a nifty little app called Zendone. It syncs with your default Evernote folder (where anything potentially actionable goes), and everything you put into that folder shows up in your Zendone inbox. From there, Zendone allows you to process each item, where you can turn it into an action, archive it to a selected folder, delete it, etc. You can add due dates, and it syncs with Google Calendar. It's currently in free beta, and they have an iPhone app out, with an Android version coming soon. Hooray!! Anyway. HIGHLY recommended, and greatly simplifies the whole process!