I am not going to count anime as cartoons, since they are too different and in a different league, in my opinion.
So therefore, I have to really look back on a cartoon that made an impression on me that I could honestly say was the best....
I'd have to say Teenage Mutant Ninja Turtles. The only reason is because I remember them the most, and because I bought into the merchandizing (toys, cards, movies etc) when I was a kid. It was one of the leading shows I liked, and definitely one of the most popular at the time.
If given other choices as well, I'd say Tiny Toons Adventures, Chip N' Dale: Rescue Rangers, and Sonic the Hedgehog (both versions).
I remember even older shows, like Count Duckula, Inspector Gadget, Carebears, He-Man, Glowworms, Strawberry Shortcake, My Little Pony, etc., but vaguely.