Zotero is a tool for organizing bibliographies. I use it to not only manage bibliographies, but also manage books and articles I read in general.
Recommended Add-ons
- ZotFile: essential extension for managing file attachments
- Better BibTex: generating citekeys, auto-exporting bibliography, etc
- Zutilo: bulk edit utilities
Zotero also supports customizing PDF annotation export; see note templates.