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.
Paws for Trello - The best way to use Trello on your desktop
GoodGantt - The best Gantt chart for Trello®
TunnelVision - See your next Trello tasks every time you open a browser tab
StandupScreen for Trello - Turn a magnetic whiteboard into an interactive Trello board
Airtable - Airtable works like a spreadsheet but gives you the power of a database to organize anything. Sign up for free.