The best open source alternative to Zotero is JabRef. If that doesn't suit you, our users have ranked more than 50 alternatives to Zotero and 18 is open source so hopefully you can find a suitable replacement. Other interesting open source alternatives to Zotero are Qiqqa, Paperwork, BibSonomy and ZoteroBib.
Bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format.
Qiqqa is a free research and reference manager. Search for, read and annotate your PDFs. Then review your work, write up and create bibliographies instantly.
BibSonomy is a system for sharing bookmarks and lists of literature (BibTex format).
ZoteroBib is a free service to help people quickly create bibliographies without installing any software or creating an account.
A new FREE citation generator. Automatically create bibliographies, references, and citations in APA, MLA, Chicago, Harvard, and over 8000 more styles with a totally free and no-ads citation generator.
I, Librarian is an online service that will organize your collection of PDF and office files. The service focuses on central management of PDF documents suitable for real-time collaboration in research teams and companies.
KBibTeX is a reference management software primarily for BibTeX which is typically used in conjunction with TeX/LaTeX.
BibDesk is a bibliographic reference manager for Mac OS X. BibDesk is designed to help organize and use bibliographic databases in BibTeX .bib format.
Scientilla is a new approach to give the scientific community an open, free, accurate, tidy and up-to-date production reporting solution.
Bibus is a bibliographic database. It uses a MySQL or SQLite database to store references. It can directly insert references in OpenOffice.org and MS Word and generate the bibliographic index.
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Open source, clean, robust. Works best with BibTex/Latex environment.