As if it hasn't been said enough, Batman: TAS. Only caveat was that I was a little agitated when WB brought it back, but with the timeline suddenly advanced (didn't care for the new Robin that much), several of the characters graphically redesigned (Timm was allowed to go all-out with his style, which didn't look quite as good as when they reeled him in a bit for the original run, Catwoman for example looked quite daft, and even had a different look out of costume) and sometimes had different personalities (Ivy getting all girly-girly with Harley and squealing during the Christmas shopping episode)... But I was still glad to get it back, at least for a little longer.
As for the others, I liked Spider-Man and X-Men both, but Spider-Man didn't get so tethered in previous plotlines (or at least flashed-back to them to explain them more), even though it still had permanent advancements in the plot (MJ and Peter getting married)... But sometimes Spider-Man did get a little short-changed in terms of animation (framerate drops) and the repeats of it now airing on Toon Disney are edited, I think. (I've read that they removed a lot of the buildings blowing up and similar things.)
Still, it was a pretty good era for animation. And I think it's getting back into an era like that, which is nice to see. For a while there, it was like they ran out of ideas for US series, so they'd just butcher some uninteresting anime (whatever they could get cheap), and throw out one or two other basic ideas that were worthless and unimaginative. Kids are often smarter than that, so I can't imagine just what they had to watch for quality weekend fodder. Not to mention how many networks had given up showing cartoons in the morning.