TMNT, Thundercats, and Voltron (lions) were my favorite as a kid. A little later you had X.O. Squad, Pirates of Darkwater(i have on dvd), X-Men (not that new stupid one), and, for a short time, Silver Surfer back in the early to mid-90s.
Other cartoons I found amusing were Ren & Stimpy, Earthworm Jim, Eek the Cat, Two Stupid Dogs and C.O.P.S. When I was real little, I like the Gummi Bears.
Those were the most memorable shows, but I grew up watching all those 80s Hanna-Barbara cartoons and other shows on USA. Jabber Jaws, Captain Caveman, Quick Draw McGraw, Smurfs, Jetsons, Yogi Bear, Flintstones, Johnny Quest (almost forgot that one!), Grape Ape, Hong Kong Phooey, Herculoids, Jem(my sister loved it), GI Joe, Snorks, Muppet Babies, GoBots (admit it, you watched them too), Tiny Toons, Rescue Rangers, Ducktales, Tailspin, SWAT Kats, Biker Mice from Mars, and let's not forgot Space Ghost (before he went coast to coast). I think there was a show with the Flintstones as babies too.
Not sure when these came out, but I thought they were very good however weird they were:
Phantom 2040, Aeon Flux, Reign the Conqueror.
And.... in case anyone wanted to know, Jonny Quest movie (zac efron as jonny, Rock as Race), the Smurfs(Neil Patrick Harris, Jeff Foxworthy, Katy Perry), and Hong Kong Phooey are all scheduled to be released sometime in the next 2 years.

"Any sufficiently advanced technology is indistinguishable from magic" ~ Arthur C. Clarke