Megas XLR!
Samurai Jack
One Piece
These definitely should be re-run. Almost everyone loves the first two, and the largest problem with the third one was bad regionalization and censorship that can now be safely ignored in late-night blocks.
Naruto
I don't think they should re-run Naruto, though. It carries a stigma now, and I don't remember it being that great either.
Bobobobobobobobobo (however you're supposed to organize that)
Given the nature of the show, I doubt that any organization matters.
Zatch Bell
Speaking of the nature of shows, does anyone else just now realize how fucking weird Zatch Bell was? It made just enough coherent sense to make the weirdness even worse than Bobobobobobobobo.
Spirited Away (might've been somewhere else, but probably toonami)
I remember it being on CN, but I'm not sure if it was Toonami. Doesn't matter, running Miyazaki films is the kind of thing that just doesn't fail. Probably because Miyazaki is awesome in all ways that one can be awesome.
Prince of Tennis (Toonami Jetstream, don't remember seeing it on tv)
Despite everything else, I think this one might win the title of Weirdest Show of All Time. I'd like to see film of this getting pitched to a group of executives, because it must have been one hell of an argument to get an anime about tennis approved.
Star Wars Clone Wars (original miniseries, not the current differently animated one nor the movie)
Is that good at all? I never watched it, and I treat everything related to Star Wars with caution these days.