Toggl - Toggl is an online time tracking tool. It features 1-click time tracking and helps you see where your time goes. Free and paid versions are available.
Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
Harvest - Simple time tracking, fast online invoicing, and powerful reporting software. Simplify employee timesheets and billing. Get started for free.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
RescueTime - Time management software that shows you how you spend your time & provides tools to help you be more productive.
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.