The murder in the hotel from "Entrée" is another reference to ''The Shining''.
The scene in the second episode where Will kneels next to a semi-decomposed person right before they reveal themselves to be alive, with a gasp, is remarkably similar to a scene in the crime-thriller Se7en.
In the same episode, when Jack finds out someone called him from his own house phone to play the recording of Miriam again, he rants about how the Chesapeake Ripper was "In my house, in my bedroom, where my wife sleeps." This is almost a word-for-word quote from The Godfather Part II, when Michael is complaining to Frank Pentangeli about the assassination attempt on him.
In Buffet Froid the killer is a girl with Cotard's syndrome. She's played by Ellen Muth. Cotard's syndrome is a mental illness where you think you are dead. Ellen Muth basically plays a dead girl, just like she did on Dead Like Me (a series created by Bryan Fuller). Even the names, Georgia Lass (Dead like Me) and Georgia Madchen (Hannibal), are basically the same. "Madchen" (or "Mädchen") is the German word for "girl" and "lass" is a synonym for "girl".
At one point, Hannibal says 'the feast is life,' likely a reference to Dracula and 'the blood is the life.'
In "Sakizuki"', Hannibal looks down on the human "mural" and its creator from an opening at the top of a grain silo. When seen from below, it's reminiscent of how God is depicted looking down on humanity in medieval art. For examples, see Annunciazione by Pietro Perugino, Annunciation by Benvenuto di Giovanni.
Katherine Pimms, from "Takiawase" is named after another beekeeper from a Bryan Fuller show. Kitty Pimms was the fake name Chuck first used in Pushing Daisies' second season opener, which also involved bee-related murder.
In "Kō No Mono" the opening scene is of a flaming body (stated to be Freddie Lounds) in a wheelchair rolling down the ramp of an underground parking garage. It's almost an exact re-creation of the scene in Manhunter with Freddy Lounds as a flaming corpse in an office chair.
Also in "Kō No Mono" are Mason Verger's blood red surgical scrubs, a nod to the uniforms in Dead Ringers. This is actually a double shout-out, as Katharine Isabelle (who plays Margot Verger) played the titular role in American Mary, who in one scene also performed a rather unconventional surgery wearing the same red scrubs.
Hannibal flips a coin to decide whether he should save Bella from her suicide attempt, filmed the same way as the iconic coin shot from Wonderfalls.
Train scene in Episode 5 of Season 3 is very simmilar to a scene in Double Indemnity. Also close-ups of actor's face fading and looming over the next shot seems to be taken straight out of cinema noir.
In episode "... And The Woman Clothed In Sun", during Dolarhyde and Hannibal's phone conversation, Hannibal asks "Did he who made the Lamb made thee?", a reference to William Blake's poem The Tyger.
There are a lot of similarities between Will and the younger Professor X in X-Men: First Class and X-Men: Days of Future Past. Will's "pure empathy" is not unlike Charles' mind-reading power (and since Will's brain contains an abnormally high number of mirror neurons, this would make him a genetic mutant), their Blessed with Suck "gift" can cause them a tremendous amount of agony, and they're both tormented by a love-hate, emotionally intimate, homoerotic friendship with a violent man of equal intelligence who has physically harmed them (Hannibal for Will, Magneto for Xavier). Both characters are dedicated to saving the lives of others, but occasionally their actions are morally questionable. In terms of their altruism, Will takes care of numerous stray dogs, while Professor X provides shelter and education to runaway mutants. As a bonus, Hugh Dancy looks somewhat like James McAvoy (both actors are brown-and-wavy-haired, blue-eyed and possess Pretty Boy-like features), so after Hannibal's debut, Dancy became a very popular fan casting choice for Brian Xavier should the X-Men Film Series ever decide to show Charles' father in a flashback.
Many have noted that Siouxsie Sioux's and Brian Reitzell's "Love Crime" which plays over the final scene and end credits of "The Wrath of the Lamb" episode sounds almost like a James Bond theme song. It's most reminiscent of Garbage's "The World Is Not Enough," Adele's "Skyfall" and Sheryl Crow's "Tomorrow Never Dies."
There's a few nods to the works of Naoki Urasawa. Will Graham's introduction scene where he re-enacts the murder scene he's investigating in a suburban home is almost identical to inspector Runge's introduction in Monster. The use of antlers as a Calling Card heavily resembles Pluto, and the Stag Man looks like an organic version of the title character.
The name "The Chesapeake Ripper" may be a subtle reference to "The Bay Harbor Butcher" in Dexter (another show about a serial killerVillain Protagonist who helps law enforcement stop other serial killers). Much like in that show, the name is given to Hannibal when the police can't figure out his identity, but he manages to get it pinned on one of his colleagues after he frames them for his crimes.
Actually, the name Chesapeake Ripper originates from the 2002 movie adaptation of Red Dragon.