Samurai Jack is probably one of the best animated series I've ever seen. It takes the limited frame animation that characterizes so much animation and actually turns it into a strength, the style and cinematography is so strong. Some really great episodes and characters. The episode with Scotsman is worth the price of admission.
Recently released on DVD is Danger Mouse. Great British animated series about a James Bondish Mouse Super Agent and his incompetent aid Penfold. Great British humor.
Batman The Animated Series is quite good. Some classic stuff there. No DVD collections out for JLI/JLU to the best of my knowlege though. I'm not as impressed with JLU though, but its been enjoyable, and you'll probably appreciate the Superfriends in-jokes.
Invader Zim is worth a shot. Nominally for kids, there's a lot of really funny stuff in it. In my favorite episode Dib (kid who's classic conspiracy nut) decides to blow the lid on a "Bigfoot" style character called "Chickenfoot" who he feels is giving "Paranormal Investigations" a bad name. When he tracks down the paranoid and fearful creature, it turns out that he's just a guy who's stuck in a chicken outfit. As the panicked Chickenfoot runs away, Dib yells after him "Chicken Foot, come back! You're not a freak, you're just stupid!"
The Venture Brothers, still being re-run late at night on Cartoon Network. It's basically Jonny Quest gone horribly, horribly wrong and it is funny as HELL!!! DVDs should be out some time next year. My highest recomendation.
Megus XLR, might still be able to find this buried on Cartoon Network's schedule. American parody of all the Giant Robot series ever made. 20 something grease monkey from Jersey finds a timewarped Giant Robot from the future and rebuilds it. Then the aliens who were using it to conquer the Earth show up and want it back. Along with all sorts of other galactic menaces that have a seeming total distain for property values in Jersey. Not that Coop (the grease monkey), Jamie his slacker best friend or Kiva - Hard as Nails warrior woman from THE FUTURE ! (but easily confused by the 21st century), have any greater respect.