I'd agree with the comments about org-mode. I was a die-hard vi(m) fanatic until I tried org-mode. This little bit of elisp was so powerful that I switched to emacs for all my notetaking and writing (though it was a bit painful on my hands until I got the hang of it). To those of you who used to use OmniOutliner and kGTD: think of org-mode as these programs on steroids.

Org-mode offers multiple ways to manipulate and access your data. Outlines + tags + chronology/calendar/diary + links + tables + todo keywords + (of course) the all powerful grep. The best feature: you can put unlimited, free-form text under any outline point. The second best feature: it's a piece of cake to export your outline (or any portion thereof) to html, with all links nicely preserved.

The plain text outline format is great because it enables me to work on small tidbits of text within my project outlines, to jot notes to myself, to keep simple tables, etc. Then I can gather all my loose ends with the very flexible agenda commands. The extra bonus: integration with web-browsing and email within emacs. Using remember.el, I can clip any snippet from another document/website/email into my main outlines--together with a nice link to the original.