in addition to what was already suggested I use a notebook and a pen to keep track of interesting classes and write notes about them, like sort of an index, and I draw few flow charts.
I used to be this way. I found that working in an editor using asciidoc/markdown is way easier for me. Copy/paste is faster than pen/paper. Also, I can write down notes and snippets of code to make life easier when I am trying to show someone what is going on in the source. Another advantage is I edit things to reflect the current state of the source and not get messed up by older notes/writings.