The scene at the witch's hideout in the deep forest, with the music to boot. The potion the witch gives to an old woman makes said old woman's head inflate, propels her in the sky then turns her into her younger self.
The hallucinations the witch causes on Godefroy. And she cackles all the way through.
Jacquart's ordeal in Middle Ages is both funny and frightening (being chased by villagers with Torches and Pitchforks who want to Burn the Witch!, being locked in a dark dungeon with rats, being tortured by an inquisitor and so on). Being a Fish out of Temporal Water from the 20th century in this era is much worse than the other way around.
Friar Ponce, the inquisitor. He has a creepy pale skin, and he has people tortured and burned for "heresy" or "sorcery", even though it's toned down by his medieval moron reaction to the moo box and misunderstanding of Jacquart's confessions under torture.
When the King's men are looking for Godefroy to punish him for using sorcery in 1124, they look for Eusaebius first. They find his mummified corpse in his bed, with his daughter telling them where Godefroy is - stranded in 1793.
Nobles being beheaded with the guillotine in the courtyard of the prison of Issoudun during the Reign of Terror, while others wait their turn watching through the barred windows as heads keep falling.
Too much crossings of the corridors of time caused Rapid Aging on Godefroy and Jacquouille, and tumors grow on their bodies as a result. By the end, Jacquouille nearly suffocates from the hideous goiter its causes him.