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

Elyse - The free version allows up to 30 tags.

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.

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

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

Leap - With Leap you find things based on your natural memory of that file.