I use a personal wiki, with sections for each project, and a todo list and inbox of physical papers organized in the GTD fashion. I use delicious.com extensivel

I use a personal wiki, with sections for each project, and a todo list and inbox of physical papers organized in the GTD fashion. I use delicious.com extensively to track and tag websites.I keep a small moleskine and pen with me at all times and carry around an iPhone, which syncs my todo list with my computer. As I work, I keep another larger moleskine for each project for transient notes, calculations and thoughts.