Among many cultural and historical jokes interwoven in the plot, one occurs when Professor Munro says to Dr. Lister, "your breath is appalling." Although the timeline is somewhat off, with Lister being of a later generation than that portrayed during the events of the film, he was nonetheless the pioneer of using carbolic acid for the sterilization of surgical instruments and cleaning of wounds during the 1860s. This effectively revolutionized surgery and saved the lives of countless patients who would otherwise have died of infection or had to have limbs amputated due to gangrene. He is also who the famous anti-septic mouthwash product Listerine is named after, hence the ironic joke about his breath being appalling.
David Tennant was originally cast as William Hare but had to drop out shortly before filming began because NBC, for whom he had recently shot a TV pilot, declined to release him to shoot the film for fear of scheduling problems if the pilot was picked up early.
The dog seen in the first Graveyard scene with Burke, Hare and the militia, is a reference to a famous Edinburgh story. Greyfriars Bobby was a Skye Terrier who in 19th-century Edinburgh spent 14 years returning to, and guarding the grave of his owner, John Gray. The movie accurately shows him as being a Skye Terrier and also shows his master's name on the grave he guards, John Gray.
An obscure joke occurs early in the movie, when Burke & Hare are unmasked as a pair of confidence men since their "Irish moss" is revealed to be cheese mold - a foolish substitute, since they could've used Scottish moss. But the real point is that such molds really can cure some infections as was claimed, and if Burke & Hare hadn't turned to grave robbing then they just might be hailed as the 19th century discoverers of Penicillin.
In the scene outside of the university, before the meeting of Monro and Knox, there is a nod to Dan Aykroyd, who was originally rumored to be in the film. As the doctors are walking to the building, they all greet each other in the same fashion as in the "Doctor" scene in Spies Like Us (1985).
The poster of Isla Fisher's character Ginny as Macbeth is very close to a famous photograph of Eva Le Galliennne as Hamlet (also a woman playing an eponymous Shakespearian character who is originally a male). They share the same stance - full body shot, face on, legs planted firmly in the ground - as well as a similar costume in the trousers, boots and cape.