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.
In Section Seekers of Perl Wisdom