Reference management software is developing in a direction that I don't think is that necessary: PDF annotation, which I have yet to find an implementation that I prefer to a regular PDF reader, but there could be some exceptions. author suppression, "see also" prefix or suffix), collaboration, and ability to work well with writing software in a way that does not interrupt my train of thought. What I look for in a reference manager is ease of use, ability to customise templates for output styles, stability, modification of in-text citations (i.e. Wikipedia keeps an open entry on reference managers that might be of interest to you. Here, I get a bit more specific about requirements useful to social science researchers. Again, I am a Mac user, so other experiences and options might be better suited for users of other operating systems. I will take a look at several reference managers that I have tried out and let you know some of my reflections on them. This section follows Part 1 on writing tools.
I think they have to be chosen together and compatibility among them has to be considered before deciding on both. Reference managers have to play nice with your writing tools.
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