In many cases I'm listening to some free instrumental music that I could use in a game, and then I see images in my head - these images lead to a story. Or I walk in the Nature, and the same happens
So in moments when I'm relaxed, inspiration comes.
I'm usually writing down at least the puzzles, so that I know where the player can pick up an item, where to use it, what the player has to solve before he can do something specific etc.
For bigger games, I draw some sort of maps, and write down important things on them, so that I know what I'm doing when I'm starting to create the game with AM.