Needing to find a tried-and-tested GTD application, I finally discovered Emacs’ Org-Mode. It’s a planner, a note-taking application — and more. I’ve taken to using it to generate most documents — whether they’ll end up as text (for email) or LaTeX (for reports). Amazingly flexible and well-documented.
You’d want to install the latest version, rather than relying on the version bundled with Emacs (since version 22) — otherwise some features described in the documentation simply won’t work (e.g. quick-selecting the initial state of a TODO item).