I usually read a document in four passes - one to get a global understanding, then deeper reading - almost like I am conversing with the author, creating and follow up on action items (searching for more items, applying what I have learned, etc.) and finally reconciling with other references on the same topic I happen to read in the future.
I want an easy way to keep track of all of this. Ideally, I envision a separate status bar for each of the phases described above. Perhaps four horizontal bars each shaded for regions where I have already done the reading. From my side, when I open a pdf, I will specify which of the above four activities I am doing and also specify that I am done with a particular page. Ultimately, I want to be able to have a snapshot of where I stand with each of the documents I am reading so it's easy to just pickup.