When Hannibal (Mads Mikkelsen) hears a knock on his door in the morning, he remarks that the last time he'd had a knock that early, it was a census taker. This alludes to the famous scene in The Silence of the Lambs (1991) where Hannibal Lecter (Anthony Hopkins) states that "A census taker once tried to test me. I ate his liver with some fava beans and a nice chianti."
When Will Graham (Hugh Dancy) is asking Jack Crawford (Laurence Fishburne) what it is that the Chesapeake Ripper does, this is reminiscent of a conversation in The Silence of the Lambs (1991) between Hannibal Lecter (Anthony Hopkins) and Clarice Starling (Jodie Foster) when Hannibal is trying to get Clarice to understand Buffalo Bill's motivations.
Futamono is typically a soup.
When Dr Bloom is playing chopsticks, it is an homage to the Columbo episode, Etude in Black.