His work on COT wasn't very good and basically finished off stop motion in movies.
First off,
Clash of the Titans was the only film where Harryhausen had assistant animators rather than doing all the work himself, so maybe that's why you perceive a change in the quality of the work.
Second, there were many major uses of stop-motion in cinema after CotT, mostly the work of Phil Tippett at ILM. There were the tauntauns, AT-ATs, and Rancor in
Star Wars, there was
Dragonslayer, there was the mine-car sequence in
Indiana Jones and the Temple of Doom, there was the flying-bike sequence in
E.T., there were the devil dogs in
Ghostbusters, there was the bat Gremlin in
Gremlins 2, etc. Probably the last great stop-motion special effects set pieces in a live-action film were Tippett's work in
RoboCop 2.
What "finished off" stop-motion was the advent of practical, realistic CGI. When Spielberg was making
Jurassic Park, he intended to use stop-motion for the full-length, running, jumping, and other dinosaur shots that couldn't be achieved practically with Stan Winston's on-set animatronics, but then ILM's computer graphics department demonstrated that they could do it more convincingly, and so Tippett's team ended up using digital "puppets" instead of latex-and-metal ones. (Actually the JP dinosaurs were animated using the equivalent of stop-motion techniques, since the animators worked with armatures covered in position sensors rather than latex skin, manipulating them the same way they would work with stop-motion puppets, but inputting their position data into computers rather than photographing them. So it was kind of a hybrid of stop-motion and CG.)
