The most visceral reference to the prequels in “The Force Awakens” comes at one of the most impactful moments in the film. Prior to the events of the film, Kylo Ren turned against the Jedi, and all of Luke Skywalker’s apprentices were killed. During Rey’s Force vision, we glimpse the grizzly destruction and, although it doesn’t take place in a Jedi Temple, the bodies scattered around, killed by lightsabers, certainly evoke one of the most shocking sequences in the prequel trilogy, the execution of Order 66, which gave the clones the word to wipe out all the Jedi in the galaxy. With a worshipper of Darth Vader in charge, emulation of his most grizzly acts is a foregone conclusion, and this reference to the end of the new Jedi only enhances the repeating cycles of the films.
There are many more references to the prequels in the films, from podracer flags and background elements to thematic similarities and story structure, but this list sums up the best of the best.
