1. Avatar: Great storyline, wonderful characters with good development to match and beautiful artwork. This wins hands down.
2. Bruce Timm's BTAS, TNAB, BB, JL and JLU. The first three series captured the dark feeling of Batman and made all of this encounters with villains and criminals intense to watch. As for both of the Justice League series, they were also able to capture a good sense of dark for their action storyline, but I also liked how they gave some attention to different superheroes that don't have their own series and may possibly never will.
3. Gargoyles. I don't remember much of the show, I only saw it when ABC Family had Jetix, but I did love how unique the story was with being dark and continious as well. Of course, there was a great amount of good action there as well.
4. TMNT 2k3: Some good humor and some great animation for the fight scenes gives this series so many great moments and episodes.
5. W.I.T.C.H: Such an enjoyable show. I loved the clear feeling of the animation and I did enjoy the fights with the different magic powers. Too bad I never got to see the rest of the series once Jetix moved to Toon Disney.