1. Pueblucho - FEZ code



In the church, at the top of the steeple (requires Goat Climb) there is a small room with markings on the wall. This is in fact a message written in the code used in the game FEZ, and reads "Be sure to drink your Ovaltine".


2. Santa Luchita - QR Code


(Image credit to user Sanch)

In a small cave accessible through a small tunnel (requires Rooster Transformation) there is a large QR code on the wall. When scanned, it says "Congratulations! You successfully identified and scanned a QR code! Great Job!"

Before suggesting any additions, please note that this is not a comprehensive guide!
While Guacamelee! is absolutely chock full of various references (especially around Santa Luchita, which are generally extremely blatant), I have selected some of what I felt to be the more subtle references that myself and other players noticed whilst playing through. Many references are purposefully left out for the sake of brevity. No doubt there are others I've missed. With this in mind, please let me know if you have found something missing that you think would be suitable for this guide.

• 1 - Forest del Chivo - Metroids
  
  
  
  
  
  
  
  
  
  
  
  Around Uay Chivo's hut, there are many of these statues depicting Metroids, the titular enemies from the game series that obviously heavily influenced this game. This references is accompanied by the Choozo statues, another blatant Metroid reference, the first of which is found just past this screenshot.
  
  
• 2 - Santa Luchita (Chicken Thief's hideout) - Booster (Super Mario RPG)
  
  
  
  
  
  
  
  
  
  
  
  Booster[www.mariowiki.com] (thanks Jirin/Valtane)
  
  
• 3 - Deserto Caliente - Cactuar (Final Fantasy series)
  
  
  
  
  
  
  
  
  
  
  
  These enemies are often found around desert areas in various Final Fantasy games.
  
  
• 4 - Pueblucho - VVVVVV
  
  
  
  
  
  
  
  
  
  
  
  Credit to user Murphy.
  This painting shows the crew from the game VVVVVV.
  
  
• 5 - Tule Tree - Majora's Mask
  
  
  
  
  
  
  
  
  
  
  
  Credit to user DeusExMachina.
  These flowers bear a striking resemblance to Majora's Mask[en.wikipedia.org] from the titular Nintendo 64 game.
  
  
• 6 - Temple of War - Castlevania
  
  
  
  
  
  
  
  
  
  
  
  Note: another of the same mosaic can also be found in the Forest del Chivo. Credit to user Dominicum
  
  
• 7 - Sierra Morena - Nyan Cat
  
  
  
  
  
  
  
  
  
  
  
  This reference seems rather fitting, as this is where you are first required to use the Goat Fly ability, leaving you flying across the sky just like a rainbow pop-tart kitty.
  Nyan nyan nyan nyan nyan nyan nyan nyan nyan nyan nyan nyan nyan nyan
  
  
• 8 - Sierra Morena - Journey
  
  

This character appears to be one of those from the PSN game Journey[en.wikipedia.org][/i], lying collapsed just before the summit of the Sierra.