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.
Shrink for Github - A macOS app for your Github issues
Create Issue Branch - Automates the creation of issue branches on GitHub
Gitscout - A beautiful Github Issues experience for macOS
REVISR - Git Management for WordPress : keep track w/ version control
GitHub Reader - A quick way to browse GitHub issues and pull requests.