The Black Heterodyne is member of House Heterodyne, though very little is known of this individual.
While Agatha and the others are underneath Mechanicsburg in the Heterodyne the viewer can glimpse in one strip a door in the background labeled "DO NOT OPEN. The BLACK HETERODYNE WITHIN". Who or what the Black Heterodyne was (or is) has not yet been revealed, and we can only speculate on what would happen were the door to be opened (though almost certainly nothing good...).
Later on, Carson von Mekkhan tells Wooster that there is in the crypt. But fortunately, they aren't going to see him today. He doesn't say anything about it being the Black Heterodyne, but that would be a really good reason for the sign.
The Novel Edit
Agatha H. and the Voice of the Castle offers a few additional bits of information about this fellow: One of his journals (as read by Professor Tiktoffen) comments that things would be much easier if "everybody didn't have those purple insects crawling in and out of their faces all the time." He also visited "the Subterranean Kingdoms" and brought back a sampling of Bloodbats, which then established themselves in the Mechanicsburg area, or at least inside Castle Heterodyne.
Perhaps most intriguingly, he is listed as the brother of The Red Heterodyne, with whom he engaged in wide-ranging and destructive philosophical disputes. Which one of them, if either, was The Heterodyne of the era is not revealed The Subterranean Kingdoms presumably have at least some overlap with the "Unseen Empire" with which the Red Heterodyne and the Jägers fought.
His favorite color was "charred".