For a few years I have been struggling along with JabRef. It has been pretty painful, but it is free and pretty portable (runs off a USB stick). Until a couple of months ago when I started using Mendeley. Mendeley comes with an in-build PDF viewer, metadata editor and the ability to upload my PDFs to a central server, so they are accessible (to me at least) from anywhere that has the internet.
The last few months of reference-managing have been absolutely wonderful (read 'have been as as wonderful as reference-managing can be).
Recently I hit the 500MB PDF limit, a bit of a bugger. Mendeley are planning on providing bigger accounts as part of a subscription service in the future, but have kindly agreed to give me a total of 1GB for now.
The killer question is will I pay for the premium service? Ideally I'd want to keep the free tool and get it to synchronise my files to a server of my choosing (I have many GBs of storage space to play with). Failing that though, as long as it's priced about the same as Flickr (i.e. noticeably less than vimeo), then I probably will.
