The thing with the explosives on the ferries... The Joker had men inside the police force, the ones that used to be controlled by the mobsters. So they could easily have gone and "checked" the ferries, but actually just set up the explosives instead. It plays into the idea that no one can be trusted and the city is corrupt all the way up through the chain of command. It's the only realistic scenario I think, and it completely ties in with the rest of the movie (with the cops kidnapping Dent and Dawes, blowing up the judge, poisoning/whatever the commissioner, etc).
Oh, and that batbike up the wall thing was fucking retarded.