To me, Sonic SatAM gets my vote, easily. It really goes out of its way with its cast and story, making them more intriguing than they had any right to be in a show based on this property while also giving a darker, more unique take on the subject matter. Even Robotnik is badass in this (that voice, man), and that's really saying something given how goofy he and his overall design is in the games.
It even had an Archie comics series based on it, and for good reason because it's amazing. It's too bad it ended after season 2, it looked like it was setting up for something amazing with
Oh, and it had by far the best theme song of any of the Sonic cartoons. Arguably one of the best cartoon theme songs of all time, it's that damn good.
The worst is by far The Adventures of Sonic the Hedgehog. There are literally no words for how terrible it is. It's so goofy, it's painful to watch. Oddly enough, both shows came out within a year of each other and are each other's polar opposites in terms of quality. Nostalgia Critic did a great vid/commentary on the two shows.