A lot of people swear by Org-Mode (http://orgmode.org http://orgmode.org) under Emacs. Everything is contained in a text file. Org-Mode adds tags, lets you col

A lot of people swear by Org-Mode (http://orgmode.org http://orgmode.org) under Emacs. Everything is contained in a text file. Org-Mode adds tags, lets you collapse/expand sections like a folding editor, lets you search on tags, etc. As you might expect from an Emacs addon, it's exceptionally powerful.