Okay, so we all heard about those shows used to push some new toy or card game written by people who clearly want to be fired...but what about the good ones? The ones where you can tell they put more effort into entertaining rather than selling a product. I'll list a few to get us started.
Batman Beyond: Yes, believe it or not this show was originally made to sell toys. It was supposed to have a kid version of Batman and be less dark and not in the same continuity as the DCAU. As if in response to this barely any toys were made for BB.
Batman: The Brave and the Bold: A Batman show that shows what BB WOULD have been. They solve the problem of being a merchandise-driven show by ratcheting up the silly/awesome by 130%.
The Big O: Okay, in spite of having giant robot fights most people would be surprised about this. The Big O was originally made to sell already-made robot toys but, much like BB, the production staff clearly went a whole other direction.
.hack//SIGN: This one just barely counts because it was the first thing created in the .hack// franchise. While the animation is almost non-existant everything looks like it was painted by WOW players, the story is surprisingly engaging and features some of the darkest s*** to ever be shown on Cartoon Network. Plus it's one of the few shows in America that had lesbians and didn't try to tone it down. THAT takes some balls.
My Little Pony: Friendship is Magic: Hey. Hey! HEY! Come back here! I swear I haven't gone mad! Okay, maybe it'll help if I say that one of the people who animated Foster's Home for Imaginary Friends and The Powerpuff Girls created this show with the idea that a cartoon meant for girls didn't have to suck. Seriously, it's much better than it sounds.
Power Rangers: Again, believe it or not but some of the writers actually cared about what they were doing, so much so that one of the writers, Judd Lynn, QUIT when executives meddled with Power Rangers: Time Force. He did eventually come back for RPM, though.
That should do for now. Also, the original Yu-Gi-Oh! doesn't count since it wasn't originally made to sell trading cards.