I simply separate my RSS feeds into two folders - A list and B list. A list is for independent writers who only post a couple times a day. B list is for news-centric websites. I do not hesitate to simply mark the entire B list as read.
I've been doing something similar for a couple of years now. I built http://readwarp.com to manage my high-volume sites, and now my google reader's dropped from 1500 feeds to 100 low-volume must-see feeds that generate 10 stories a day.
Readwarp's an ancient hobby that I don't work on anymore. Did it seem like I was trying to convert traffic? We all know how to build landing pages with big, bright call-to-action buttons, you know.
I've long since pruned most features on the site. There's no way to import feeds, etc. It only really works for me anymore. I linked to it because it's hard to make sense of custom reading solutions without pointers to try them out.