Qiqqa is by far the strongest solution for research and managing pdf's. Zotero, named as a comparison is weak as it does not allow pdf;s to be loaded into its interface - you need to use a pdf reader, which defeats its whole purpose. With Qiqqa documents in a library can be searched together. It has excellent maps of your libraries. It is not prefect, having a few glitches, but still is the only one of its kind.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
JabRef - Graphical Java application for managing bibtex (. bib) databases.JabRef · JabRef Help · JabRef | Blog · OpenOffice/LibreOffice .
Citavi - Citavi is a program for Microsoft Windows that manages literary references and organizes organizational knowledge.
Docear - Docear
Paperpile - Clean and simple and reference management for the web. Sync your PDFs to Google Drive and cite your papers in Google Docs.
BibDesk - BibDesk is an organizational software created to help you edit and manage your bibliography. It keeps track of your bibliographic information as well as said information's associated web links and files. Read more about BibDesk.