To say that the game Guacamelee! contains a few references would be a massive understatement. The game is absolutely brimming with them.
While playing the game for review (which should be coming soon) I kept track of whatever hat-tips, homages, and internet memes that I could find in Guacamelee! Most of them should be pretty obvious. A few of them may very well be paranoia on my part.
Fair warning: Contains joke spoilers.