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.
Linear - Streamlined issue tracking for software teams
Nifty - Manage projects, work, and communications in one place.
Distiller - Distiller's hosted continuous integration platform takes the pain out of mobile development through automated build, test, and deployment of your iOS apps.
Jira - The #1 software development tool used by agile teams. Jira Software is built for every member of your software team to plan, track, and release great software.
BugHerd - BugHerd: The Website Feedback Tool for Agencies