In this series, Batman/Robin/Batgirl knows each other secret identities, but what about the commissioner? Some eps its implied he knows, some eps he doesnt know Barbara is Batgirl. Does he know Batman/Robin's secret identities?
Commisioner Gordon doesn't know any of their secret identities. Batman and Robin know Barbara Gordon is Batgirl (she contacts them as Barbara Gordon and asks if they need her help as Batgirl in the episode "The Bermuda Rectangle"). However, Batgirl doesn't know Batman and Robin's secret identities.
That's true. Gordon doesn't know any of their identities. In "Trouble Identity", when he confronts Batgirl on the theft of the converter, he has no idea that it's his own daughter. Batman and Robin know James Gordon's middle name is Worthington. And while Batman and Robin do know that Batgirl is Barbara Gordon, but she doesn't know their identities. In "He Who Laughs Last" she is brought to the Batcave blindfolded.
Now on the other hand, BatMite knows Batman and Robin are Bruce Wayne and Dick Grayson, but he doesn't know that his big crus, Batgirl is Barbara Gordon. This is evident in "Bite Sized" when he asks Barbara to contact Batgirl for him.