Etrian Odyssey released in 2007 and was a fun throwback to this sort of experience. The concept for this game is that the Nintendo DS's touch screen can be used to draw a map and keep notes while dungeon crawling. It's funny to think that it's about as old now as the style of games it was imitating then.
The 3DS also had a note-keeping system built into the main menu and usable in any game, but I don't think many people bothered.