Super Paper Mario - In Merlee's Mansion on Chapter 2-3, Mario accidentally breaks a vase and has to pay in rubees (parody of rupees) to find a replacement. Also, Mimi fires weapons in her boss battle.
Kirby series - Kirby's sword ability strongly resembles Link. Upon getting the sword ability Kirby gets a green hat similar to Link's and when he has full life he is able to use a sword beam.
In the first Final Fantasy game, there is a town named "Elfheim." In this town there are three gravestones next to a building. The one on the far left has flowers in front of it and if you press A while looking at it, it says "Here lies Link." This makes sense because it is a town of elves and everyone is dressed like Link.
Non-Nintendo Titles[]
Terraria[]
In Terraria, the Hero armour set strongly resembles Link, including a green hat, green tunic, and tights.