Free Reference Managers: Mendeley vs. Zotero
Answer
In General, Mendeley (https://www.mendeley.com/) and Zotero (https://www.zotero.org/) are very similar and include almost the same functions. They are both free reference tools, with an option for institutional subscription that enable more storage space on the cloud and more collaboration options.
They both include a a mix of a desktop software and a cloud service that can be synced automatically or manually. They are both very user friendly and allow easy importing of citations, web-clipping tool for adding citations from web pages and databases and a Word add-on.
The main advantaged of Mendeley are:
1) it is better in handling PDF files (journal/ebook resources), both by automatically extracting their metadata much better than Zotero and by allowing you to highlight and annotate them and save it within the software.
2) Its Word add-on often works better.
3) Offer mobile and tablet apps.
4) In its free version (not with institutional subscription) allows 2GB of free cloud storage (compared with only 300MB offered by Zotero)
The major advantages of Zotero are:
1) Its Web-clipping tool is much better and can more easily (one click) download citations regardless if they are PDFs or non-journal/ebook web resources (like in the case of newspaper HTML articles, web pages as citations, etc.).
2) Allows collaborating with bigger groups of people than Mendeley.
3) It is open sourced and not sponsored by any publisher.
It is also important to mention that both Mendeley and Zotero can import and export citations from/to each other or other reference managers. So using them both for different time periods or different types of materials is also an existing option (not very recommended though).