There are a number of resources that I have found useful in thinking about productivity processes and tools.
The One Minute To-Do List provides useful insight into balancing long-term effectiveness with the tyranny of the urgent. The book is free, and is a subset of Linenberger's larger Manage Your Now system.
Getting Things Done is one of the more popular modern productivity methodologies. I haven't found the overall system to be a terribly good fit for my own workflows, but the idea of an ‘external trusted system’ — not depending on your brain to remember everything you need to do — is quite valuable.
Bullet Journal provides useful syntax for managing hand-written paper notes.
Getting Things Done for Hackers adapts the GTD methodology to programming work.
Switch: How to Change Things when Change is Hard is a great book on how to make changes that last. Improved productivity habits can be one of those changes.
Wunderlist is a decent to-do list manager with wide platform support (including Windows Phone).
Trello organizes cards into lists, allowing a good visual layout of tasks in different states.
TaskWarrior is an expressive command-line task manager that is good for terminal geeks. It has a number of interesting features such as intelligent task prioritization.