Here’s a couple of examples Keep talking and nobody explodes — The most popular in the list I think
Uncle Chop’s rocket shop — the game where you are repairing your client’s rockets by following the in-game guidebook
Tin can — here you are also repairing the spaceshp but this time you are it’s capitan and you are in space in the middle of nowhere
The DS version of Ni no Kuni included a physical spellbook you’re meant to consult. JP-only, but the fantranslation made it into a PDF.