Stone tries to distract the Queen of Hearts with the Mad Hatter's riddle "Why is a raven like a writing desk?" The original intent of this joke was that there is no answer; however it became an odd sort of challenge for writers to devise clever answers. The great English writer Aldous Huxley proposed " Because there is a 'B' in both and an 'N' in neither."
Prospero speaks in blank verse (iambic pentameter), a literary device Shakespeare is famous for.
When summoned into the library room by Prospero, Moriarty compares the room (unfavorably) to the Wallace Collection. The Wallace Collection is a major UK museum full of paintings, statues, artifacts, and furniture, but very few books.
Frankenstein's Monster shows up just after Flynn and Ezekiel "steal" Zeus's lightning bolt. The original title of Mary Shelley's novel is "Frankenstein; or, The Modern Prometheus." Prometheus being the titan in Greek mythology who stole fire from the gods and gifted it to humanity.
While Flynn and Jenkins discuss the status of the library, the audience can see the words inscribed over the doors leading back into the library: "nam et ipsa scientia potestas est" roughly translates to "for knowledge itself is power". The entire episode is about the tree of knowledge. (19:53)