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.
MAXQDA - a professional software for qualitative and mixed methods data analysis
Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
QualCoder - A very complete Free and Open Source Software (FOSS) Computer-Assisted Qualitative Data Analysis Software (CAQDAS) written in Python. It works with text, images, and multimedia such as audios and videos.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
ATLAS.ti - ATLAS.ti is a powerful workbench for the qualitative analysis of large bodies of textual, graphical, audio and video data. It offers a variety of sophisticated tools for accomplishing the tasks associated with any systematic approach to "soft" data.
JabRef - Graphical Java application for managing bibtex (. bib) databases.JabRef · JabRef Help · JabRef | Blog · OpenOffice/LibreOffice .