I use it semi-frequently. In OoT I used it as a makeshift checklist so I could mark off heart containers and skulltulas I found while in bed, instead of having to turn on a computer or use a sheet or paper. --- https://www.youtube.com/watch?v=KQ9Km7WW2aE Best console war summary ever. TL;DR version at 2:05.
I used it to keep track of multi screens of data while writing up parts of my TotA shop price guide. Since it's impossibly long going to each shop to check prices, and keeping your place in the list is a pain. So it does serve a purpose, I mean now you could see a screen shot of current shop & previous shop you jotted down.
I used the Game Notes for Link's Awakening, too, TC. Except for the gravestone puzzle, and not the egg. That was the only time I ever used them, in addition to drawing a wang on another note, because the 3DS needed a simple drawing program at the time. --- PSN: Echidneys | 3DS: 4468 1242 8413 "It sucks, and you're all stupid for liking it."
I used it in Zelda:OoT to remember the Scarecrow's song, and made a map of the lost woods, then kept track of all big Poe locations and checked them off. I also used it in the Mercenaries to remember which characters I needed S rankings with on which levels. Recently I used it in Sticker Star, I mapped out the Bafflewoods, and then Sandshifter Ruins.
One time I was at the Pawn Shop and I ran into a customer for my Business and did'nt have anything to write on so I opened my 3DS and wrote his number down in game notes. He looked at me weird and asked: "What is that? Some kind of mini laptop?" I laughed: "It's my Nintendo", he said: "that's effin' cool, I want one".
Anyway, Nintendo hit on something good with game notes, I just wish it allowed you to input characters as well as write or draw. Sometimes it's a pain in the butt to try to decipher my own crap writing, and it's hard to write neatly really small with a stylus. --- If you were a boss I'd deathmatch ya in a minute!