I've tried Mendeley, Zotero and Jabref and stuck with Jabref for my masters thesis. Couldn't recommend it enough, even though haven't given Zotero a serious try.

Synced bibtex and pdfs folder in linux and windows with dropbox, worked like a charm.The best part was configuring it based on this blog post (http://griechenzicken.blogspot.com/2011/10/configuring-jabre...) and making pdf links work on both machines. I wrote a blog post about why Jabref, but unfortunately it is in portuguese (https://gtpedrosa.github.io/blog/gerenciador-de-refer%C3%AAn...).

used jabref myself a lot, mainly because it's easy to understand how it works (all state is in your .bib files). never really missed any features.