Jason comes to a broken down temple of Hermes, not believing in the gods of Olympus, and meets the priest there. The priest suddendly turns into Hermes, grows giant, and teleports Jason to the Olympus to meet the gods.
Talos was voted the second greatest movie monster by Empire readers for a reason.
The Clashing Rocks where Triton appears from the ocean and holds the rocks apart so the crew can sail on.
Jason fighting the Hydra.
The Argonauts fighting skeletons. It was the very apex of Ray Harryhausen's stop-motion art.
The entire action sequence on Colchis including the fall of Hercules and the battle with the dragon.