Every graduate student knows that moment of existential despair when the papers you’ve been reading and the citations you’ve been accumulating for a particular project begin collapsing into unnavigable chaos. Fortunately enough, a marvellous piece of software known as a citation manager can come to rescue.
Here are some elements of comparison you might consider. Both Zotero and Mendeley:
- have a desktop version as well as a web-based version,
- provide extensions (which save items into your library as you go),
- offer the possibility to upload articles, and
- generate your list of references in a diversity of styles (in both managers the accuracy of data needs to be checked, though).
Generally, the main difference between Zotero and Mendeley is that the first one is better for long-term projects because it is very stable and reliable, whereas Mendeley, although less stable, offers unmatched functionality with PDF editing, thus we can recommend it for short-term projects.
However, it is strongly advised that you try both of them out and compare on your own, just in order to see what works best for you personally.
If you are looking for more detailed comparisons that also include other reference manager software, you can consult the dedicated Wikipedia page and the overview provided by the University of Toronto.