I have a notebook full of random notes for (mostly) NES games.  It includes obvious things like passwords, but there are pieces of graph paper with maps for Wizardry, diagrams of Metroid, Zelda dungeons, strange secrets I notice, high scores, etc.  It is quite a nerdy things to do.  But if I don't make a sea chart for Uncharted Waters, I'll get lost and those sacks of sugar will never make it back to England!

I do not usually take notes while playing games, however I regularly wish I did.  I'm generally just too lazy and cluttered, and I never have graph paper around when I decide I actually want to make a map of something.

I always hated it in games when I was trying to make a map only to have my character magically whisked away to some other place and I would have no idea how it related to where I had been.  Deadly Towers seemed particularly bad about that.

Otherwise I just scribbled passwords on random scraps of paper and set them on top of my NES until I lost them.