Zube - Project management for developers.
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.
Matrify - Manage information in tables.
TaskBoard - A Kanban-inspired app for keeping track of things that need to get done.
Binary Tree - solve issues and manage documentation; no spreadsheets
Pintask - Pintask is the most customizable Kanban board.