Another Mendeley user here :)

I import articles into Mendeley and pop them into my "unread" folder. Once I've read an article and written appropriate notes for it (which I do in the "notes" section in Mendeley - I never print articles out) I migrate it to each of the several relevant folders (I treat folders more like tags, so each article goes in several folders). I often skim an article, but that doesn't get it out of the "unread" folder, so there are lots of articles in there that I'm working my way through. Only when I'm sure I've read it well enough and taken good enough notes does it graduate, which is when I "remove from collection" I believe Mendeley calls it.

I really love Mendeley because of the online storage and sync between several computers. It allows me to work from home and not worry about taking my notes with me. Their nifty little web importer is cool too, though slightly too easy. I end up with lots of articles only marginally relevant :P