A recent post from Christopher Long reminded me to mention Zotero. I had been using Mendeley but have gone back to Zotero because I found that Mendeley desktop crashed on quitting rather too often but also because of Zotpad for iPad and iPhone which I prefer to Mendeley Lite.
Zotero is a plugin for Firefox and now also for Chrome and Safari and it also has a stand-alone desktop version allowing off-line usage. For me though the extra plus is using the iPad to read PDFs of journal articles and being able to annotate them when reading in any number of the PDF apps available for the iPad. I use a couple of different ones - I like Notability (see post below) but like Christopher Long I also use GoodReader. You can annotate then return them to ZotPad and they are then updated in the Zotero library.