Taguette - A spin on the phrase "tag it!

Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.

NVivo - Buy NVivo now for flexible solutions to meet your specific research and data analysis needs. 

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.

Qiqqa - Qiqqa is a free research and reference management software. It can be used in many organizational projects from the academic to the personal to the business endeavor. Read more about Qiqqa.