I vote 2000's Sponebob, Ben 10, Teen Titans, JLU, Fairly Odd Parents, The Avatar, The Kids Next Door, Spectacular Spiderman, Ed, Edd and Eddy, Courage the Codwardly Dog, Xiolin Showdown, Froster Home for imaginary friends, Star Wars the Clone Wars (Both Shows) etc.
90s beat early 2000s by a hair, only because of Tiny Toons, Superfreak, and Animaniacs. They were seriously well-written. To me, the first few years of the ealry 00s can take on any few select 90s, but collectively 90-99>>>00-09. Avatar is my favorite of all time, though.