Both Avatar series are excellent choices. The Last Airbender is a great adventure story, while The Legend of Korra deals with adulthood and coming of age issues.
Gundam Wing, love it!!!!! If you can lay your hands on the Gundam: 08th MS Team might be a bit over the head of your kids - the material is very literary and kinda weighty, but it's got big robots.
Dragonball Z. I love this series. Your kids will love the action and root for Gohan as he grows up. You will dig on the character development and really be able to think about the spiritual implications and teachable moments the story provides. It's the cartoon I chose to use to teach my son to think about the content of the television he watches.
Pokemon. Especially the early years. Friendship, action, and a lesson in every story. The cartoon is very light, but the movies are surprisingly deep and occasionally disturbing.
That's kind of the standard fare these days. Avatar and Dragonball Z are both currently airing on Nickelodeon. Pokemon is on Cartoon Network.
Disney Channel/XD just wrapped up Gravity Falls. It's an excellent show that's heavy on an adult brand of weird, with all kinds of stuff to look for. If you've got the Disney Channel/XD, the current crop of Marvel cartoons (I know, superheroes.....) just keep getting better, with punchy episodes and epic season-long story arcs.
Want to dig for gold?
Cardcaptors. Magical girl Sakura and her friends are tasked with recapturing the spirits that have escaped from the Klow cards. Good luck finding this series. If you do, let me know.
Thundercats. Eye of Thundera, give me sight beyond sight! Get the recent Cartoon Network release. There's only one season, but it's got a long story arc and Lion-O gets to make some really hard choices. Plus, Will Friedle voices Lion-O.
ReBoot! One of my very favorites, now available in a complete series box set. Season 1 is standard kids fare, but seasons 2, 3, and 4 get really dark as Enzo Matrix learns what it takes to be a Guardian. The season 2 finale *still* takes my breath away.
Yu-Gi-Oh! Available on Netflix. This is the same kind of show as Pokemon. Strong lessons in friendship and personal morality, but with a really dark spiritual undercurrent if you examine the core concept.
"The rational mind is dangerous; the Christian mind is devastating."
Opposing Forces powered by Fate!