I stumbled on this.
Reference management software is an incredibly useful tool for researchers and academics. It solves two problems that are otherwise very frustrating: (1) organizing and searching PDFs of journal articles, and (2) properly formatting a bibliography when writing a paper with citations.1
I wrote the first version of this post back in 2015, and I’ve periodically updated it since then (see below).
The biggest change since 2015 is that some reference managers will now directly interface with Google Docs – if you were using Microsoft Word and “track changes” to collaborate on manuscripts, you should strongly consider switching to a Google Docs-based workflow.
The other big change since 2015 is that it’s feasible now to use a web-based reference manager without a native macOS/Windows app. This is due to improvements in web technology, like pdf.js.
I am sticking with Zotero for the time being. PapersApp/PaperPile isn’t for me. Their annotation is good but I am happy without it. I have a better workflow.