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the biggest nod to B89 is clearly batman throwing joker off the building, and that's the one "nod" to B89 that has been discussed where nolan might be trying to outdo burton.  nolan has said that burton's biggest mistake was killing off the joker, batman's greatest nemesis.  someone said how it was a "complete film" and they didn't know how good or bad it was going to do so they couldn't leave it open for a sequel, but you don't have to leave a movie open for a sequel by killing the bad guy.  just so everyone's clear, the dark knight was almost not made.  nolan does one movie at a time, and when he was filming BB he has no knowledge of where the next movie would go if at all.  i heard rumors of how IF a sequel were made joker wouldn't be in it and he would be saved for the third.  nolan never knows what he's doing in advance, but he didn't kill scarecrow in BB, and ra's could still be alive, probably not.  so yeah, joker being thrown off a building and being caught to stress that batman won't kill him might be trying to out do burton, but out of all the nods to B89 that's probably the only one.  all the others can be seen as either out of respect, or it's batman so there are going to be some similarities regardless.