I love the episodic nature of Cowboy Bebop, mostly how the show reveals itself one episode at a time. The universe is so cool, and the way the show builds layers to help create a history without a main plot ever being the focus is extremely skillful. How the later episodes connect the characters, and help them get over their pasts is also expertly crafted. A common complaint with Cowboy Bebop is that it has no story because it's episodic. That's like saying The Simpsons has no story: the setting is what builds it all up into the show people loved. That said, I know it's not for everyone, but I always thought it was ahead of everything else animated and a tv show that it isn't the aforementioned Simpsons.
Samurai Champloo is well made, but it's...not really that great in the long run. Unlike Bebop, it doesn't have a made up world. It takes place in historical Japan so there's nothing to expound upon.