After a few seconds of deliberation, I realized that Eradicator was probably too obscure of a reference, but the backstory of the Eradicator does kinda fit, what with the whole purity of Krypton thing that could tie in with Jor-el talking about human blood on the element. Still, I think it would be cool if it were the Eradicator.
Brainiac wasn't one of my considerations because, yeah, he's from space, but this ship seems pretty clearly Kryptonian.
I like Doomsday for the same reasons I like Eradicator: Kryptonian origin and a mad-on for Kal-el.
I don't think Zod would come in a ship like that. It's too three-D.
Of course, it could be something completely (sp?) new.