OK... suprised no one mentioned this one...
The Littles.
I also was getting into Beakman's World for a bit as a grown up. Not really a cartoon, but it was fun.
I like the Real Ghostbusters, and the other Ghostbuster show for a while.
Gummy Bears needed more air time, and a longer run. It seemed to end all to quickly. Darkwing duck was alright, Rescue Rangers rocked, Talespin was cool, Ducktales didn't do as much for me, and the new kid Goofy was... god, that was bad.
I like the Voltron with the various cars and things to make up the guy, the Lions was crap.
Ren and Stimpy was genius, and the Cow and Chicken from the same creators was great, specially I Am Weasel and I R Baboon.
Tiny Toons was a great re-imagining of the great Looney Tunes cartoons, and had superior writing that some of today's regular tv shows need to take note of. I watched the Looney tunes cartoons also, along with the older Tom and Jerry cartoons. First time I seen the "new" ones, I flipped the station.
TMNT was great for a while, but the repeated fight against Shredder was becoming stale and the jokes that were bantered about between the turtles didn't come off right after a while. The movie (first one) was awesome for it's day, I was in the Navy then and seen it in the theater for 5 separate viewings. I still wonder what happened to the actor that played Casey.
When Batman TAS came on... that was a great show that could have been a prime time cartoon. Mark Hammil voicing the Joker, man that rocked. The Justice league was good, of what I saw of it.
Saturday cartoons in general has almost been killed off. Anime crap like Pokemon, Power Rangers and the card game one that has the three lettered words strung together. Then Congress passed some dumb arse law that had the news programs come on Saturday mornings and had stupid pre school shows like Telly Tubbys and Dora be introduced into the mix, and the shows that actually were made for mere entertainment went away. The WB (CW now) still has it's line up, but has half of it from over seas (they are still showing Pokemon!) along with Sonic (Bad cartoon from a great Video Game) and new TMNT that was and is pretty entertaining. It runs Sunday morning over here, or did. I don't watch much these days.
EDIT forgot Animaniacs. That show rocked, and had Pinky and the Brain and other good side shows.