Batman:TAS
Superman:TAS
Batman Beyond
Justice League
Justice League Unlimited
Green Lantern:TAS
Young Justice
Animaniacs
Freakazoid
The Flintstones
The Jetsons
Looney Tunes
Scooby Doo
Super Friends
Superman (Max Fleischer)
Tom & Jerry
As far as JLU goes, it is automatically inducted into any "Best of" lists, for me, because it contains one of the single greatest Batman moments in ANY medium. It's in the episode "Epilogue", where an older Amanda Waller talks to Terry Mcginnis about his predecessor.