in reply to how do you organize your notes?

For keeping track of day to day programming, I used to just keep a todo.txt file open and write down everything I needed to remember, like what to do next, and what command line details I used for various things.

A plain text file is quite enough for this.

Nowadays I use Emacs org-mode and keep the same things in an outline structure instead. Highly recommended if you alreay use Emacs. Also, make sure you try out the fantastic table edit mode.