Special thanks to Rediscover the 80s and Banzai Retro Club for the argument on Twitter that inspired this list. I'm sure they'll have a lot to say about it.
Honorable mention 1 - GI Joe: The Movie
Honorable mention 2 - The Raccoons
Honorable mention 3 - Disney
Without further ado - my favorite themes:
Jayce and the Wheeled Warriors
Adventures of the Galaxy Rangers