When I was using them I kind of had a system.

One for political news, which had /r/news, /r/worldnews, /r/worldevents, /r/world{etc}, /r/foreignpolicy, /r/nottheonion, etc.

One for gaming, which had /r/gaming, /r/{insert consoles I'm playing on here}, /r/{insert games I am currently playing here}.

One for tech news, /r/technology, /r/futurology, /r/apple, /r/windows, /r/unix, /r/openbsd, /r/freebsd, /r/linux, etc.....

One for legal news, /r/law, /r/patents, /r/copyright, /r/history, /r/eff, /r/yro, /r/privacy, /r/cyberlaws, etc.

One for the crazy people, /r/conspiracy, and all that crazy shit that spawns off of it (kind of fun to read every once in awhile how nuts some people are).

So really, it was to group a bunch of like reddits together, but you could do other things too. Some days I just wanted to read tech news and legal news, some days I was just there for gaming. Some days I was just there to watch the crazy people go nuts and feel a bit saner. Some days I'd open up two windows and make them side by side, one with one feed, one with another.

I'm noticing similar issues here. Like for instance, I want to follow music tastes across the site but I don't want that mixing in with my regular feed, I'd rather have that a separate feed, food tags, etc.