For the most part Gotham is pretty faithful to the history of the Dark Knight laid out in the comic books, drawing heavily on the source material (sometimes a little too heavily) and making only minor changes like the casting of Sarah Essen or the addition of characters like Fish Mooney and her subordinates. One of the few major changes to established continuity they make, however, is quite the doozy: far from being a mugging gone wrong, it appears that the murder of the Waynes seems to be part of some larger conspiracy, a straight-up assassination ordered by...someone. Which isn't an angle we've seen taken on Batman's origin before, and we kinda like it. From the looks of it we're not going to find out who the culprit is, either. At least, not the guy who actually pulled the trigger. Which is good, because you shouldn't know. He's just meant to represent, like, Bruce Wayne's ongoing war against crime. If he got revenge on that one dude, he might feel some sort of closure and hang up the cowl. At some points the comics identified the crook as a guy called Joe Chill, and even forced Batman to team up with him for reasons too stupid to explain here. In the Tim Burton film the killer was Jack Napier, who later became The Joker, who Batman later wound up killing. Some have suggested that this might have been another stealth introduction of a future villain from the Caped Crusader's rogues gallery, as the call for the hit clearly came from somewhere other than the crooked police department, the suspect Mayor, or the criminal empire of Carmine Falcone. Bruce Wayne describes the killer (and we see him) as wearing a "black mask", which more imaginative fans are seeing as foreshadowing of, well, Black Mask, a sadistic crime boss and supervillain who in the comics once pulled a dead guy's eye out and fed it to his wife. And if Fox are prepared to air such a scene on primetime network television, then they have our full support.
Tom Baker is the Comics Editor at WhatCulture! He's heard all the Doctor Who jokes, but not many about Randall and Hopkirk. He also blogs at http://communibearsilostate.wordpress.com/