I honestly can't remember many great shows from my childhood but there are a few excephions. Let's get the most obvious one out of the way first:
-Avatar: The Last Airbender
It's been said time and time again that this is a great show. I really enjoyed it far more than any other shows, so I was surprised to see that, aside from the occasional toy-based Anime (like Yu-Gi-Oh, Beyblade, Bakugan etc.), very few shows went for the same form of storytelling as it. Everything had to be a comedic episodic show where almost no episodes had any relation to eachother.
Of course, that's not an inherently bad formula for a cartoon. Shows could easily make that work, like for example:
-Courage the cowardly dog
Looking back at it, I'm surprised I wasn't scarred by some of the seriously creepy stuff Courage showed in some of its episodes. I guess this show is responsible for me not being phased that much by traditional horror, it exposed me to so many creepy elements at such a young age that I couldn't even understand was meant to be absolutely horrifying. I'm guessing that for a while I've thought "if 8 year old me could watch this without being scared, then it's gonna take a lot more than some bloody abomination in a horror game to scare me!".
-Time Squad
I'm not very sure about how this show holds up. I have very fond memories of it, but I don't think it sired that much in my time. I only remember it airing st convenient times when I was like 6 years old, and only airing late at night when I was about 15. Last I saw of it, it was still pretty fun, even with the Norwegian dub.
-Bakugan Battle Brawlers
As a kid, I loved this show, it was fun seeing characters sort out their differences with ridiculus over-the-top incarnations of a childrens card+figure game. Looking back at it, it's sort of a guilty pleasure to me. I know it basically devolved to an advertisement of the card/figure game it was trying to sell and the battles eventually turned into a race to see who could spam the most cards to see how high of a number they could get, but there's something about the story that I can't quite put my finger on, that sort of makes it fun watching to me, even now as a 20-year-old man. Maybe it's just the nostalgia? I'm not sure, probably.
Other shows that I don't have as much to say about but still fondly remember: Xiaolin Showdown (thanks for reminding me about the name, Diophatine), Teen Titans, the Justice League cartoon, 90's Spider-Man cartoon and Samurai Jack.