There's going along with the narrative flow.
And then there are actual plot holes that require giant leaps of logic, or fast editing to ignore them, fan explanations, things that require characters to teleport, be omnipotent, or use a deus ex machina, that just don't hold up when you think back on it. (So Dock Ock was supposed to get Spiderman… so the throws a car at Peter Parker in a resteraunt... who he doesn't know is Spiderman...) As long as the movie can suspend your disbelief the first time through and carry its own momentum, as long as it CAN explain all its own questions, and so you can be entertained, it did its job. (Momento is ONLY good once, for instance)
But good movies can hold up to a bit of scrutiny and answer their own questions, and great ones don't even beg those questions due to editing problems in the first place. Not having a character explicitly state something and leaving it to the viewer to figure out... is NOT the same thing as just jumping around and having no answer at all. (And I enjoyed LOST, so I know something about that particular argument.)
Dark Knight was full of those sorts of plotholes and leaps in logic. (Someone posted a 40 minute video on it yesterday.) I still haven't seen Rises, but its easy to believe more of the same.
@Taggerung:
How Joker set up those bombs is not important or relevant to the plot at all. Whats important is that he did it and impact that it has on this city and batman and it pushes the story further.
A crazy man who admits he doesn't plan things out, still somehow repeatedly planning things out to a meticulous split second timing in the exact path that all the action is going to flow IS jarring eventually, since it does basically require omnipotence on his part, and a ridiculous ammount of elaborate and discreet behind the scenes work.
Driving a bus out of a bank with smoke trails and NOBODY even flinching, no police coming, and the requisite split second timing needed to kill each member of the gang on cue in location and time it to enter the chain of buses right off the bat is something that just doesn't make sense. It's cool the first time you see it and makes you go "Oh wow, that was a great plan! Joker is awesome" But the second time, you have to stop and go… "Wait... that defies all logic and plausibility. How did he...?"
Dark Knight is fine (though 20 minutes too long.) But it DOES fall apart some on second viewing. It doesn't mean the movie failed, since it can keep your interest and the momentum and obviously a lot of people like it and overlook these things and they aren't completely glaring. But... it also means its not the near perfect intricately plotted crime thriller its hailed as either, since logic and plausibility just have to be thrown out the door for some of the set pieces to work, and editing has to hide some of it.
@Taggerung:
It's like complaining that John Hammond creating dinosaurs was a stupid idea to begin with in Jurassic park and therefore the movie is just a giant plot hole. You're not accepting the rules of the fiction. You're adamantly refusing to do that and because of that you will find tons of things you consider plot holes but they aren't.
You accept there are dinosaurs in Jurassic Park, because thats the main thrust of the movie and the explain it at length how its done and that's the ENTIRE point. You accept that. (In DK you accept there's a man in a bat suit, and a crazy clown man blowing stuff up.)
You don't however have to accept the fact that the T-Rex cage keeps changing, or that the monorail driven cars somehow ended up going backwards, or that we're supposed to hate the lawyer making sense JUST because he's the lawyer, or that Nedry despite knowing all the dinosaurs on the island doesn't know about the spitter, or that nobody ever used their guns.
You don't have to accept that the Joker was left at a party with no resolution, or that he can can set wires in the exact path of airborne helicopters ahead of time, or that security is completely stupid and inept, or do the impossible amount of setup and split second timing most of his plans require, or that Batman can physically beat the crap out of him without him even flinching. Or that the Joker knows Batman is gonna save Harvey so he shoots a bazooka in the direction of Harvey's vehicle because he knows Batman is gonna jump out of nowhere to intercept the shot. He knows how quick Batman is and how a-little-less-quick the police is so that he can send Batman to save Harvey and send the police to fail to save Rachel. And worst of all, he knows that a police officer will stay with him INSIDE his prison cell so that he can take him hostage and eventually kill everyone. If the police officer was not retarded, he would have been watching him from outside the cell, from the other side of the mirror-window.
Do these things break the movie? No, it carries you in the flow and is fine. But do those things seem weird and illogical with some afterthought? Do they eventually sink in so you think about them whenever you see the movie, and thus hurt the movie some? Yeah, they do.
Doesn't mean the movie is bad or that someone being bothered by these things just wants to hate the movie, but it does mean the problems are there, and its fair to call the film on it when people are saying its realistic, flawless and intricately plotted.
Citizen freaking Kane has the MASSIVE plot hole in the first minute that nobody was in Kane's room to hear him say "Rosebud", and so the entire investigative premise of the movie doesn't work. But you can forgive that because the rest of the movie is pretty much flawless.