Basecamp - A simple and elegant project management system.
ActionSprout - ActionSprout provides tools and training to help nonprofits realize their goals on Facebook.
Asana - Asana project management is an effort to re-imagine how we work together, through modern productivity software. Fast and versatile, Asana helps individuals and groups get more done.
Merit - Merit Network is a nonprofit member-governed organization providing high-performance computer networking and related services.
Redmine - Flexible project management web application
Eleo - Eleo is an online donor management software.