If you've seen my post on motivation hacking then you know that I'm using Beeminder to track a wide variety of things. I try everything I can to automate the tracking - import learning data directly from Duolingo, have a custom script poll WaniKani for my current level, track how long I practice piano by reading midi output over USB, integrating with Runkeeper to track how often I run, etc.
Now I've also found a good way to track the papers I read: Every paper I'm interested in I add to [cached]Mendeley. Then once I've actually read it I can add notes, and most importantly copy it to a special [cached]"Paper's I've Read" group. All papers in that group show up in a RSS feed, which I can then track with a similar IFTTT recipe to what I use to track posts on this blog.