It's hard to choose. NBC, CBS, ABC, Fox, and Kid's WB all had great lineups at various points.
NBC gave us Smurfs, Alvin & The Chipmunks, ALF, Saved By the Bell, and a few others;
CBS had Muppet Babies, TMNT, Bill & Ted's Excellent Adventures, Pee-Wee's Playhouse;
ABC had Sonic SatAM, The Addams Family, Superfriends, Scooby Doo, Darkwing Duck, The Wild West C.O.W. Boys of Moo Mesa and Beetljuice among others.
Fox gave us Batman: TAS, Animaniacs, Attack of the Killer Tomatoes, Power Rangers, X-Men TAS, and the Tick;
And Kid's WB had Men In Black, Batman Beyond, Pokemon, Legion of Superheroes, X-Men Evolution, etc.
There's no way to choose, I loved all them. When they put their heart into it, all of them had superb lineups. But in the later years and the execs didn't care, the lineups sucked. Hard. But I still can't decide.