Yojimbo - Yojimbo makes keeping all the small (or even large) bits of information that pour in every day...

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

HoudahSpot - Advanced File Search Utility for Mac OS X

Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.

DEVONthink - DEVONtechnologies develops DEVONthink, DEVONagent, and other Mac and iOS apps for document and information management and web research.

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.