Visual Effects of Awesome: Medusa. If it doesn't look that impressive to you, consider how hard it is to get the highlights cast by flickering torches right when they're being cast on something created by stop motion animation! Even today, more than 20 years later, special effects experts the world over are in awe of what Ray Harryhausen accomplished in that scene.
When Bubo rescues Pegasus from Calibos's goon squad.
When Andromeda insists on going with Perseus to find the Stygian Witches, she shows she's an Iron Lady instead of a Damsel in Distress.
Perseus: I'll set out in search of the Stygian Witches on my own.
Andromeda:No. We will ride with you as far as their shrine. It is a long and perilous journey.
Andromeda: You are not my lord and husband — not yet. In the absence of the Queen, it is I who'll command.
Pegasus rising up out of the water after the battle with the Kraken, you can tell he was preening for all those who were watching.
Near the end, when Perseus seems to be down and out and when it comes time for the Kraken to be unleashed, Zeus sighs in defeat and tells Poseidon to release the Kraken... while sneakily putting up a figurine of Perseus to have him get a Heroic Second Wind.
How does Perseus solve the riddle and earn Andromeda's hand in marriage? He cuts off Calibos' hand which has the item needed to solve it and throws it down onto the steps, pretty much in front of the goddess favoring Calibos and all the people that worship her.
During the final battle, as Perseus is attempting to slay the Kraken, Hades shows up to interfere, splitting himself into a half dozen of what this troper assumes are Erinyes and engaging Perseus (riding Pegasus) in a massive aerial battle for Medusa's head. Just as it looks like one of them is about to take out Perseus, the Erinyes is snatched out of the air. Pull back to reveal Those Two Guysriding one of the giant scorpions from earlier in the movie. That's right, they kept a giant scorpion! Best. Mount. Ever.
Also from the remake, Calibos's Dynamic Entry. He gets the drop on Perseus's gang, grabs a Red Shirt and tears him in half with his bare hands.