The upgrade "9th color" could be a reference to Terry Pratchett's Discworld series, in which there are 8 colors, implying a step up from even that.
Part of the flavor text for the Prism upgrade Gem Polish ("Truly, truly outrageous.") is a reference to the 1980s cartoon series Jem, specifically the opening theme. Some believe that it may also be a reference to the League of Legends champion, Taric, but in actual fact, this too is a reference to the theme from "Jem."
The name of the last achievement, Praise the Sun, is a reference to a famous quote from the game Dark Souls.
Inside of the code for the beta version of the game, you can find an achievement "The Dark Side of The Moon" with flavor text "oh god", which requires to have 1000 prisms. It is not added to the final game and Orteil left a commentary after it which says: "this is a joke I promise". Its name is also a reference to the Pink Floyd album of the same name.