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by j2h6mW 4705 days ago
It's not exactly a stand-alone app, but Org-mode in Emacs is pretty excellent for this. I like it because I can take text files with me anywhere (even onto a smartphone if I'm using a syncing app like SpiderOak).

Here's a link to get you started: http://orgmode.org/worg/org-gtd-etc.html