The numbers stenciled on Hannibal's (Mads Mikkelsen) asylum coveralls are the same number on Lecter's (Anthony Hopkins) coveralls in the The Silence of the Lambs (1991).
When Dolarhyde picks up Reba at the bus stop there is an ad for a dentist. It has an open mouth showing the teeth saying Ahhhh. Open wide. Biting is part of Dolarhyde's (The Tooth Fairy) MO.
All the episodes in the Red Dragon arc contain lines from the movies.
Episodes 8-12 of the third season are named after the various iterations of William Blake's Red Dragon watercolors.
Hannibal admits to Jack Crawford that he didn't expect to ever see him again. In the novel "Red Dragon", and the films "Manhunter" & "Red Dragon" -- Jack Crawford and Hannibal Lecter do not share a single scene together. Some of Crawford's dialogue is also lifted right from Will and Hannibal's initial confrontation in the novel.