When I was much younger I became familiar with Getting Things Done via the then popular Lifehacking movement. Getting Things Done is a system for taking control of your projects and life by getting all the stuff you need to do into a single system. While I am not a perfect adherent, the general principles have proven durable and useful since I started using it in my law school years.
As far as software goes I have settled on keeping everything in an app called OmniFocus. The advantage of OmniFocus besides the fact that it follows the metaphors from the book is that it is easily accessible. It has been written in a way that I can easily add and edit stuff on my Mac, iPhone, or iPad. For email, using Gmail plus its keyboard shortcuts have shown themselves to be important to staying near Inbox Zero.
Ultimately the three principles that are most useful to managing all my projects are: breaking things down into smaller pieces, keeping the information needed to do tasks in as few disparate places as possible, and being comfortable with a backlog. By organizing the things to be done and minimizing the work needed to do them, I am able to do more things when free time makes itself available. By prioritizing the things I am able to do more of the useful stuff. Ultimately these strategies are a tool for feeling more in control, and that is what makes the difference.