1. W.I.T.C.H. (Great story and characters, a central story which develops each episode, plenty of plot twists, creative powers and abilities, destroys many cliche tropes found in other shows, and a nice rich fantasy world with it's own mechanics and laws. So far unparalleled in American children's cartoons)
2. Beast Wars (Best Transformer series in the franchise. It blends action, story, and comedy and is not afraid to kill off characters or introduce new ones into the fray, and has a set goal with develops quite nicely and ties back into the other Transformer series)
3. Justice League + Unlimited (Serious, action-packed superhero cartoon with plenty of mature, envelope-pushing plotlines. Eventually gives focus to the lesser known DC heroes which probably never will get a [good] show about them)
4. Teenage Mutant Ninja Turtles 2003 (Dark, serious, and cinematic-esque version of the turtles that is closer to the comic. Plenty of developing story, even if it does have some bland episodes and went on quite longer than it should have, but still entertaining)
5. The Venture Bros (Blends action and comedy quite well, and an adult cartoon so it can get away with more in each category. Despite this, it's not just a senseless gore/sex-fest and there's an actual story there)
6. Spectacular Spider-Man (Best Spider-Man cartoon to date. Nice fights and potential for some interesting plotlines, need to see more for a true representation for the story and how the plot twists will be handled)
7. Wolverine and the X-Men (Looks to be quite promising from the episodes I've seen, a more serious and realistic approach to the mutant racism and X-Men mythos, and also showcases some lesser-known mutants)
And I'm shocked that you put South Park on your list, too. I thought you said that you completely dropped it.