Zotero

Zotero collects, organizes, and cites research: one-click capture from your browser grabs papers with full metadata and PDFs, the desktop app organizes collections and notes, and plugins insert citations into LibreOffice and Word in thousands of styles. The built-in PDF reader with annotation extraction (added in v6+) made it a full research workspace, and it’s run by a nonprofit.

Free cloud storage caps at 300MB — beyond that you pay Zotero or configure WebDAV sync for attachments, which is doable but fiddly. Group libraries and institutional workflows are solid but less polished than paid EndNote support contracts provide. None of this stops it being the default recommendation for students and researchers.