I'm not sure these tools are really about rationality per se, but anyhow the LW-community seems to have many people who are interested in this kind of thing - myself included.

My personal favorite to bring to a Swiss army knife fight would be emacs and, in particular, org-mode, which keeps me sane in the daily maelstrom of information coming to my desk, in the form of emails, meeting notes, action points etc. org-mode can do clocking (to see how long I'm spending on tasks), all kinds of reminders, todo-lists and can even check which of my 'projects' currently don't have a NextAction defined (as per GTD). It can display all these things in many ways, say, only '@phone' items or only items I've been waiting for for more than a week.

It even integrates with my e-mail, and I have hooked it up with my web browser, so with a few clicks I can store interesting snippets (with a source link of course) for review later.

The downside? Well, you'll have to learn emacs first, which does many things differently from other programs. All can be customized by writing a little lisp to make it behave as you want, but I understand that could be a non-trivial barrier. Having crossed that barrier, I would say that it's worth it (bias alert).