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If you are using emacs, give org-mode a try. I also keep this todo lists in git repo to sync among various machines that I work with.

I use org-mode and symlink ~/org/ to my dropbox folder. I love this setup, though I really wish Dropbox had an iPhone app and a public API. Both have been promised for quite some time.

I've written a web-thingy for this. I enter a bunch of tasks in the text area and then I can either continue editing them from text field or use GUI. Bonus: it understands (with some restrictions) natural language ("due two days from now", "project blablabla.blehblehbleh", "high priority"), unlimited nested projects and is available from anywhere :)

I have tried RTM on and off, but I usually end up back at this method as well (though I use x for completed tasks). Add sync with something like Windows Live Sync, SugarSync or Dropbox and it's portable enough, too.