I've organically come to a system that works pretty well for me.
I browse HN, reddit, Zite (iPad), and sometimes click on links in my fb feed. That's my 'inbox'. Then:
1. Anything I feel like reading right away, I read.
2. an actual article, usually more long-form, I add to my instapaper list.
3. an article that might be interesting, but not right away, or anything else that is worth saving, but not useful right away, I add to Pocket.
4. for any comment pages, or articles that somehow don't go through step 2 or 3, I add them to my OneTab list (by far my most-used chrome plugin). Often these are just things I can't read right away, but I'll probably look at later in the day, or things that instapaper can't handle (HN comments).
5. anything that really stands out, I either add to my OmniFocus inbox, or to my Wunderlist inbox (Because I don't have OF on my phone).
With that done, here's how I process stuff:
1. when at my computer, I tend to first check my OneTab backlog. I open a few tabs, and read through them. This is generally during work breaks or lazy moments.
2. On the road, particularly short commutes, I read instapaper articles. I intentionally kept myself from getting internet on my phone so I'll keep from aimless browsing. Interesting snippets or articles then go to my Wunderlist inbox for later processing.
3. On longer trips, or significant downtime, I generally look at Instapaper for the 'better' material.
4. every once in a while, or when I'm reminded of something I read a while back, I check my Pocket 'dump' for the relevant material.
All in all, this kind of just started happening through use. I didn't agonize over a workflow, and I'm not sure it's optimal. But it works pretty well.