One of my absolute favorites was probably Beetlejuice, the animation.
Now that I think back at it, the plot of these episodes was usually kinda silly, but I guess back then it must have been pretty cool.
Another favorite was Ghostbusters.
Still love it to this day, the humor is funny, if not a bit cheesy, but this is alot of fun to watch. Not to mention, this is way better than ghostbusters: extreme (lame) and the 80's ghostbusters show that nobody likes to talk about.
Other than that, there's all the other usual stuff, spiderman, batman, etc. Naturally, there were also a couple of shows you had to watch because they were so retarded. Hammerman is a very good example. The intro itself warns people away from watching it.
Why did MC Hammer need a cartoon? The song itself is a strange mixture of sad and hilarious, and I have blocked out any actual memory of the show itself. Another one was Street Sharks.
I blame Ninja Turtles for the existance of this show. Apparently people were under the impression that mutated animals were the thing to do for a while, which also bred shows like 'Biker Mice from Mars'. ...Although they were from Mars, not mutated. Same difference though really. As for the Street Sharks, the very concept of the show was silly. Men get turned into shark-people that immediately start spewing shark-related one-liners and fighting crime. I always felt bad for the city they operated in, since mostly, all they did was cause a shit-load of property damage. If nothing else, their theme song was simple and half-way decent.