Hello. I'm an academic and do almost of all my writing in LaTeX or straight text, using textmate. I've become a new fan of TextMate's use of TODO.

It's really simple. You imbed literally the word TODO in a comment in the text of anything in your project:

% TODO 46. META TASK: Flesh out bibliography, right? more references?

and then hit shift-control-T and it will find all the TODOs and make them into one html doc, with links that take you to the doc! Beautiful!

Something coders have used in IDEs for a while, but brand new to me in this context.

(When you're done, you change the TODO to CHANGED and those are cataloged, too...)