First of all, in ALTTP and the games before, no fairies followed Link around. But in the comic, Zora sends Link off with a fairy, Epheremelda. Then, in Oot and MM, a fairy follows Link around. Coincidence? Maybe.

Then, during the battle with Ganon in the comic, Zelda fights alongside Link with Roam's bow. Now, if I remember TWW correctly, Zelda is also fighting Ganon in the final battle, also using a bow.

I'm pretty sure that someone got the ideas for these portions of the games from Shotaro's comic. I think that's pretty cool. There could also be similarities between the comic and some of the gb games, but I haven't played those, so I don't know. Maybe there'll be similarities in future games, too.