Dave the Barbarian come to mind. I feel that it was never given its chance, as it was an overall funny Disney-toon that couldn't compete with whatever was on at the time.
I don't know if Samurai Jack is obscure enough to qualify, but the animation is flawless and it has a plot to boot.
A favorite of mine that I think qualifies is My Dad the Rock star. It had a premise that got me in easily, a kid with a father as a rock star, yet he tries to be a normal kid. It was created by Gene Simmons himself, and even though it aired on Nick, it never got picked up by Nicktoons network.
Tutenstein too, and also the TimeWarp Trio, but I really would go for My Dad the Rock Star.