The only serious, large note-making endeavor that I've undertaken is with Star Control 2 (The Ur Quan Masters).
Now in this day and age of the Information Superhighway, you can find an ungainly amount of information about games. But that is not the joy of The Ur Quan Masters. To get that sense of being a star ship captain and exploring the unknown, I kept a log of all the important information needed in that game. You will get nowhere in UQM if you do not.
Things to be tracked include information like star system coordinates, types of stars likely to contain rich deposits of lucrative elements, locations of enemies throughout the galaxy, who is allied with whom, who are enemies with whom and why, and comments and hints gained from conversations with alien races.
Star Control 2 / The Ur Quan Masters is so enormous that I can guarantee the odds of playing an identical run-through as someone else are very small indeed. Well worth a play-through, either with the 3DO or PC original, or with the enhanced free modern version (UQM).