Trello - Infinitely flexible. Incredibly easy to use. Great mobile apps. It's free. Trello keeps track of everything, from the big picture to the minute details.
MIP Fund Accounting - MIP Fund Accounting is a true fund accounting software solution that nonprofits across the world are using to make sure that every dollar is used to the utmost - from donation to the final project.
Basecamp - A simple and elegant project management system.
Sage Intacct - Intacct is a cloud-based accounting and financial management system that is designed for the businesses of all levels.
Teamgantt - Intuitive project planning and collaboration. Beautiful Gantt charts, task-level communication, file sharing, resource management and more.
QuickBooks Desktop Enterprise Nonprofit Software - QuickBooks Desktop Enterprise Nonprofit Software is Quickbooks answer to nonprofit organization's fund accounting problems.