There was that episode with Todd Stashwick as Richard Sionis, the corporate guy who was making his employees fight for promotions, and who fetishized masks. I'm guessing he was meant to be the father of Roman Sionis/Black Mask.
I think we've seen Zsasz, Riddler, Penguin, Two-face, Catwoman, Joker, Scarecrow and maybe even the Professor Pyg guy ( I really don't like Grant Morrison's additions to the Rogue Gallery - tho' I like Damien Wayne). Who else have we seen? Fish/Butch are new to the Bat-universe, right?
Fish and Butch are new, yes. As for Pyg, we've seen one or two people in pig masks, but they were associated with other villains, so I don't know about that.
We've also seen the Electrocutioner, a minor Batman rogue in the comics. And one of the people he experimented on was Amygdala. The Dollmaker was referenced in episode 2 and is slated to return. The female assassin who went after Selina and Bruce was evidently based on Copperhead, according to Wikipedia. And of course various other non-supervillain antagonists like Falcone, Maroni, and Flass.
Plus Milo Ventimiglia is slated to appear as a character based on a comics villain called Ogre. I'm unfamiliar with that character.