NOTE: This guide is for the Western releases of the games. If you need QR codes for the Japanese releases, google them.
QR codes are used in the 3DS Yo-kai Watch games to receive Crank-a-kai Coins and special key items that unlock additional content such as special Yo-kai and Quests. QR codes were distributed via Yo-kai Medals, Japanese magazines, and social media. As there are so many QR codes from the toys, I will not cover them unless they give something particularly special (Translation: I'm lazy and don't want to cover them).
Unlike future localizations, Yo-kai Watch 1 does not accept Japanese QR codes; the game will only accept QR codes released for the West.
If you need to befriend Gilgaros, here is a video by YouTuber JohneAwesome with a lot of QR codes for Crank-a-kai coins.
There are five Yo-kai locked behind QR codes: Sapphinyan, Emenyan, Rubinyan, Topanyan, and Dianyan. These five are collectively known as the Jewelnyans. For San Diego Comic-Con 2016, Hasbro released the exclusive Jewelnyan Set, which contains the five medals for the Jewelnyans and a figure of Dianyan. Scanning their QR codes will get you special Crank-a-kai Coins that, when cranked, get you special Bells to fight and befriend the Jewelnyans daily.
Yo-kai Watch 2 has significantly more Yo-kai locked behind QR codes compared to Yo-kai Watch 1.
Yo-kai Watch Blasters
Yo-kai Watch 3