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.
Evernote - Bring your life's work together in one digital workspace. Evernote is the place to collect inspirational ideas, write meaningful words, and move your important projects forward.
Create Issue Branch - Automates the creation of issue branches on GitHub
Tyke - Mac menu bar app that @torrez really needed to take notes
REVISR - Git Management for WordPress : keep track w/ version control
Notion - All-in-one workspace. One tool for your whole team. Write, plan, and get organized.