I use NetNewsWire since it's available on both desktop and iPhone, and it syncs with Google Reader which makes it available pretty much everywhere. The Google Reader sync also means I can use convenient extensions in Chrome to add feeds—currently using Sharaholic as all-in-one for URL shortener, Delicious, Google Reader etc.
(I don't like the interface of Google Reader, so that's why I'm using native apps.)
Haven't put much thought into the actual organization to be honest, at least not as much as my GTD system. The folders are my subjects of interest, such as "Business", "Design", "Writing", and "People" for specific personal blogs.
I probably have too many feeds since I have 300+ unread posts at the moment and not much time to read...
EDIT: Almost forgot, I use Instapaper to save posts for reading later. It's nicely integrated with NetNewsWire.