Todoist - Todoist is a to-do list that helps you get organized, at work and in life.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
Remember The Milk - Remember The Milk is a task and time management application for mobile devices.
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
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.
Freeplane - Freeplane is a powerful and free software for building mind maps.