I wasn't sure whether I was remembering Dino-Saucers or something, else, but quickly looking at Wikipedia I think it was the episode Primordial Plot. It ripped off Jurassic Park after the book but before the movie!
I think I vaguely remember Glamour Girls and Cold Slither but I'm not sure if I'm just thinking of other face/swapping and subliminal message/evil rock band stuff I saw as a kid.
I think I remember There's No Place Like Springfield. Is there a scene where they tell him that Lady Jay was killed in action? If so then I definitely remember it.
I must never have seen the Golden Fleece episode, because I can't believe that I ever could have forgotten that.
Aside from the movie the story I remember best, and one that I've seen again a couple times as a teen/adult, was the 5-parter "Arise, Serpentor, Arise!"
Did you ever watch the awful DIC episodes? The story I most remember was the 2-part anti-drug episode. G.I. and Cobra join forces to take on drugs. Normally nobody died in the series, but somebody did in that episode, because you know what's more dangerous than war? Drugs!
Here are some clips:
the first few seconds of this one sound like Judas Priest. Maybe the used that riff more than once but it's close to the "You don't know what it's like," part in Breaking the Law.