Shoke PDF manager
Further to previous posts (one, two) on how to organise collections of papers in PDF format, here’s a post at lifehacker describing Shoka, a PDF library tool. From a glance it looks like Shoka ticks all the right boxes - it’s free and open-source, and is written in Java so it should run on all platforms (it uses Java Web Start at the moment). It looks like Shoka is under heavy development right now, so it might be worth keeping an eye on any updates.