My personal favs are...
The Rhedosaurus from the Beast from 20,000 Fathoms
The Ymir from 20 Million Miles to Earth
And Gwangi from The Valley of Gwangi
Tough to say, really. I have my favorite characters, the ones I think are his best, and the ones that seem to advance the story the most or provide the most memorable or dramatic scene.
Standalone favorites: 1) Rhedosaurus, 2) Cyclops #1, 3) Saber Tooth Cat
"Best": 1) Cyclops #1, 2) (tie) Hydra, Medusa, 3) Baboon
Most dramatic: 1) Skeletons (any of them), 2) Medusa, 3) Ymir.
I would have to go with:
1. Trog ( Big suprise, right?) It is a beautiful model and the subtle "personality" animation is incredible
2 Allosaur. One Mllion Years BC. Great Energy!
3 Ymir. This is an iconic character and the range of performance, from the haunting hatching to the savage
attack on the farmer, is a benchmark of stopmotion.
Medusa; she's the only Harryhaussen monster I find genuinely creepy. Furthermore, I'd argue her scene in Clash of the Titans was some of his best technical work - he even managed to get the flicker from the torches and the shadows from the pillars.
Indeed, that's my main reason too; and I say a big part of why she is so scary is because Harryhaussen did some masterful work with the lighting in that scene - just remember how she stalked in and out of the shadows and that the only part ever clearly lit was her eyes.
3. Sabre Tooth Tiger
It's hard for me to choose anything after my #1 and #2, but I always liked the movements of that cat--very realistic.
1. Mighty Joe
Talos, the Siren Figurehead, the Cyclops.
1. The Cyclops
2. Mighty Joe Young
3. The Evolution of the World T-Rex
Has to be the ymir, mighty joe, & skeletons ... and the worse (I know it wasn't part of the question) has got to be the stupid mechanical owl Bubo ... jbd