Teenage Mutant Ninja Turtles (The Turtles may be goofy, the villains may be goofier, but I'll be damned if April O'Neil isn't played spot on right)
Exo-Squad (One of the only cartoons I've ever known to portray not just one but to heroes of the series dying valiantly in battle)
Jem and the Holograms (I had a crush on Kimber...that and the show was outrageous. Truly TRULY outrageous. Nuff said. ^_~)
Transformers (I'm an official member of the Church of Optimus Prime. I EVEN HAVE A T-SHIRT THAT SAYS SO ^_~)
She-Ra: Princess of Power (She-Ra was my idol when I was young)
Bots-Master (My only complaint about this show was it ended after things were really starting to get good plot wise)
Robotech (Another one of the few shows that featured the heroes suffering loses in battle. The Invid Saga was a favorite of mine)
Superman: The Animated Series (This show is nominated for having THE best villain. PERIOD! I'll never forget my gasping as Darkseid vaporized Dan Turpin in front of Superman and then simply smiling afterwards)
Batman: The Animated Series (This show was dark. REALLY DARK. The villains [and even Bruce himself at times] were often tragedies in of themselves brought upon by humankind's selfishness, greed, hate, fear, etc etc. Really portrayed the darker side of human nature)