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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.
Whimsical Sticky Notes - Visual project management using sticky notes
Create Issue Branch - Automates the creation of issue branches on GitHub
Jot - The no-fuss way to take notes
REVISR - Git Management for WordPress : keep track w/ version control
Gone - An ephemeral to-do list