When comparing EndNote vs JabRef, the Slant community recommends JabRef for most people. In the question“What is the best reference manager?” JabRef is ranked 4th while EndNote is ranked 8th. The most important reason people chose JabRef is:
Free and Open Source Software
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Mature
Pro FOSS
Free and Open Source Software
Pro Organize articles based on keywords, tags, search terms or manual assignments
Pro Browser Extension
Chrome, Firefox, Microsoft Edge browser Extension. Import new references directly from the web browser with one click using the official browser extension
Pro Hierarchical collections
Group your research into hierarchical collections
Pro Regular expressions
Pro Find unlinked files
Pro Native BibTeX and BibLaTeX support
Perfect for text-based typesetting systems such as LaTeX and Markdown.
Pro Cross Platform
Windows, Mac, Linux
Pro Keep track of what you read: ranking, priority, printed, quality-assured
Pro Word and LibreOffice/OpenOffice upport
Support for Word and LibreOffice/OpenOffice for inserting and formatting citations
Pro Create Entry From XMP Metadata
Cons
Con Poor web interface
Con Expensive
Con Requires Java
Java is now shipped with the application and no longer needs to be installed separately.