I’m working on PenguinTV 3.0, and I came up with a crazy new way to select feed tags. Check out the screencast and see for yourself. I would appreciate any comments or suggestions on how to make this better.
Note: if the user has no tags at all, the new screen shows only “All Feeds” and “Downloaded Media”, and none of the other panes.
Have you looked at epiphany's (the browser) way of tagging webpages? Webpages can have more than one tag, so it automatically categorizes based on some principles of which I'm not 100% sure of. It's hard to explain how it works, because when I use it's so intuitive I've never thought about its thinking. You should try using it, and bookmarking and tagging about 50 webpages, and see how they are presented in categories.
Also, in the future they intend to allow to search for tags, which is when tags are important.