[phren0logy]

To anyone looking for an alternative, I'd just throw out there that I've been very happy with ReadCube. It's proprietary subscription software, but that's a trade-off I can live with for a great browser plugin, mobile apps with good annotation, cloud storage of annotated articles, seamless syncing across devices, and a high-quality Word citation plugin that works on the Mac.

This company bought Papers, the Mac app, and it looks like they are finally getting ready to release the desktop client based on that acquisition.

[veddox]

I used ReadCube several years ago when it was still really new (and free). Great program, very pretty interface - but it didn't work on Linux. When I switched from Windows, I had to let it go.

[phren0logy]

I mostly use the web version, and that seems to function well everywhere these days. Not sure about the desktop version, but after ages and ages they are finally getting the desktop application that incorporates their Papers acquisition, so it might be worth looking again if you like it. Hopefully, that does a better job on Linux, but that's always a gamble.

[krull10]

I've been looking for a replacement for Papers for years; it just doesn't work well anymore with the lack of attention they've given it since the acquisition. For me subscription pricing is a no-go. It's sad, I would happily pay for a new standalone Papers...