Plot holes.
Two words that can separate good movies from bad. That change opinions over whether potentially great movies were simply just good or even below average. The Dark Knight Trilogy, the Avengers, Skyfall, Prometheus, and most recently Man of Steel have all fallen victim to nitpicking fans that label these blockbusters as being riddled with plot holes.
But what exactly qualifies as a plot hole?
Strictly speaking, a plot hole should be defined as when something takes place, either a plot-related or a character action, that causes a crucial inconsistency that goes against what's been presented to us in the movie beforehand.
...but maybe it'd be easier to go through what ISN'T a plot hole first.

1) The most obvious one is the age-old debate: "In the Lord of the Rings, why didn't they just fly the eagles to Mordor?" Ignoring the fact that there actually are solid explanations for this, the biggest one is simply that there would be no movie if they did that. And that does not make it a plot hole.
Contrary to popular belief, movies aren't supposed to make perfect logical sense in the real world, no matter how "realistic" some movies are made out to be. The very nature of movies is that they are unreality. Movies are there to entertain us. To tell a story with comedy, drama, conflict, and ultimately a satisfying resolution. You can pick apart almost any movie and find something that could've been done differently that would negate the entire premise, and unfortunately there are some people love doing that. But again, that's not what movies are about.
Take Looper for example. For argument's sake, rather than having the future mob drop their intended targets back in time right in front of Loopers to eliminate them, couldn't they have dropped them in the middle of the ocean? Or in a volcano? Or any of a million other places where it'd be virtually guaranteed that they would be killed? That would ensure that Joseph Gordon Levitt's character wouldn't have a chance to screw up killing his future self, and everything that happened in the movie wouldn't ever happen. Everything would go back to normal. But that's missing the point of the entire movie. We the audience are watching precisely because we want to see something take place that's out of the ordinary in the world the movie takes place in. To see characters make mistakes, struggle to find a solution, and leave us with a sense that something was actually accomplished.
The Looper and Lord of the Rings 'solutions' are inherently flawed, solely because all the conflict in the movies would never take place. Without conflict, you wouldn't have an interesting story. Without an engaging story, you wouldn't have a movie in the first place. So logically speaking, plot holes can't and shouldn't be grouped together with these flawed show-stopping examples.
2) Implausible or extreme coincidences in movies don't make it a plot hole, either. Going back to why we watch movies in the first place, it's partly so that we are presented with an unusual or otherwise interesting story that (probably) wouldn't happen to us in real life. Whether these unlikely things happen to further the plot or just to give us drama in the most impactful way possible, it can't be a plot hole as long as it stays consistent with the rest of the movie and the world it takes place in.
One popular example of this would be many of the events that take place in The Dark Knight. The Joker is presented to be always several steps ahead of our heroes, having taken contingencies on almost every possible event that could happen. Captured by the police? Good thing he was prepared to bomb the MCU and take Lau. Helicopter flying at almost street-level guarding the entourage escorting Harvey Dent? Cue the henchman with the trip wire in the perfect position to take it down. And on and on it goes.
Sure, it's ridiculously lucky that things keep happening in such a way that the Joker keeps on coming out on top until the very end. But when you think about it, it just doesn't matter. The purpose of his character is that despite all his denials of having a plan, he has a frighteningly efficient and well thought out goal to descend Gotham into chaos. And nothing that he does goes against anything that's been established in that movie.
3) As a general rule, things that don't make much sense AFTER having seen the movie and only after putting a lot of thought into it shouldn't qualify as a plot hole either. I say this very carefully, because the caveat is that if the director and writers are able to suck you into a movie so much that you find yourself completely unable to catch minor logic gaps during the first few viewings, then they've done their job. Movies that are this engrossing are sure signs of a pretty great film because, one more time, movies aren't meant to be completely, 100% logical or foolproof.
The sequence with Jim Gordon taking the bullet for the mayor, faking his death, and then secretly leading the convoy to bait the Joker into attacking doesn't make much sense when you think about it. What exactly was the purpose of faking his death? Doing so to avoid risking his family's safety is a pretty vague answer. Who was even in on that plan? Harvey seems surprised to see Gordon alive, but Batman must have known because he obviously crashed on purpose to give Gordon the opportunity to capture the Joker. But then why did they show Batman in the shadows, seemingly mourning when the cops give Barbara Gordon the news about her husband? When would Gordon have had the time to show Batman that he was still alive and then fill him in on what he had planned?
However, even this admittedly convoluted chain of events isn't a plot hole. Things were presented to us in such a way to sell us on a singular notion at that point of the story: Gordon was dead, and Batman has to take down the Joker when he attacks the convoy. Everything that is shown has a purpose - to feed into this notion so that we get the most out of the action sequence. The bewilderment we feel when Batman chooses not to hit the Joker with the Batpod and crashes. The complete surprise when a random cop gains the upperhand on the Joker and is revealed to be Gordon. Rather than making much sense in a strictly logical way, Christopher Nolan rightly chose to create sequences that played on our expectations. Which is why most of these little irregularities didn't blatantly stick out to most people walking out of showings of the Dark Knight for the first time. The telltale mark of a great movie.

Another movie that jumps to mind is Jurassic Park. It can be argued that director Stephen Spielberg's MO is to sacrifice common sense and logic to maximize the emotional and dramatic impact of the moment. This is nowhere more apparent than the infamous T-Rex scenes. Spielberg disregards logic, physics, and geography not once but twice. In the first scene, with the rain pouring down and the group's 2 cars stuck on the track in front of the T-Rex paddock...it makes no sense that they're stuck there in the first place. The jeeps run on a single track throughout the tour, and they'd already been to that paddock earlier in the movie. Did they circle around the entire park and conveniently get stuck right by the T-Rex? And then after it eats the goat and breaks through the fence, 10 minutes later that exact same piece of land somehow turns into a 100 foot high cliff that the T-Rex can push the car off of.
And again in the climactic finale in the Visitor's Center, the survivors are surrounded by raptors with no way out. Suddenly the very same T-Rex appears out of nowhere to save the day. No one heard it coming, no one saw it coming, and yet this and the previously discussed scene are two of the most memorable scenes in the film. Why? Because it told logic and sense: "To hell with 'em!" It catered specifically to what we were hoping for, emotionally. Spielberg said it himself: if they didn't bring back the T-Rex to be the hero of the day, audiences would've rioted.
20 years ago, did some people scratch their heads and wonder how an acclaimed director could make two such blatant 'mistakes'? Probably, but it's more than forgivable because of the emotional high, the raw tension and drama it gave us and allowed us to experience. And, once again, that's what watching movies is all about.
4) This point seems obvious, but things that take place off screen, or are otherwise unexplained, are not plot holes. (Unexplained plot points and loose ends certainly have the potential to be, but only if they have severe ramifications on the rest of the plot.)
To use the Dark Knight again as an example, the scene where Joker crashes Dent's fundraiser and throws Rachel out the window, forcing Batman to come to her rescue, leaves no explanation for what the Joker and his henchman did with a penthouse full of Gotham's richest and most influential patrons. The main reason this isn't a plot hole is that there are numerous explanations for what the Joker could have done next. Perhaps he decided those people didn't figure into his plans, so he simply left. That seems absurd, but the Joker is a psychopath after all. In a way, it makes the most sense that he would do something as irrational and illogical as leaving the people alone.

In the sequel, it is left to our imaginations as to how Bruce Wayne traveled halfway across the world after escaping Bane's prison and found his way into a Gotham City on lock-down. Many fans chalk this up as a glaring plot hole, and perhaps in an ordinary action movie it would be. But based on our information of the character to this point, it can't be a plot hole.
From Batman Begins, we know that young Bruce stowed away on a freight ship after his humbling encounter with Carmine Falcone and traveled the world, with no passport and no money, in order to fully understand the criminal mind. We already know that Bruce has a talent for stealth. To state the obvious, Bruce has done things like this before. The only difference in The Dark Knight Rises is that rather than showing it or alluding to it, it happened completely off screen. Putting these facts together, it's no far leap that Bruce was able to sneak into Gotham in the given timeframe (It's obvious a significant amount of time has passed. Batman is defeated and thrown into Bane's prison in the summer/fall after their first fight, and when he comes back there's snow on the ground).
Most recently, in Man of Steel, Lois Lane finds out that the Kryptonian ship crashed in the Arctic ice is at least 18,000 years old. The movie doesn't concentrate on where it comes from, how it crashed there, why Kal-El's suit is located there...because none of that really matters.
Whatever the answers to these questions are, it wouldn't affect the rest of the plot in any way. It was purposefully left ambiguous by the filmmakers in order to devote time to more important parts of the story. Perhaps it will be expanded upon in a future sequel, perhaps not, but this doesn't make it a plot hole.
And as I understand it, a prequel tie-in released shortly before the movie came out even explained the origins of that ship while featuring a cameo from another DC hero...making this even more of a moot point. Bottom line, seemingly unexplained plot points do not always make plot holes.
So if all of these things aren't plot holes, what are?
For comparison, let's look at a few movies with legitimate plot holes.
1) Pirates of the Caribbean: Dead Man's Chest. In a movie with Disney-fied pirates, mystical and magical creatures, and high-flying stunts, only story-related issues have much of a chance of being called a plot hole.
One such gripe occurs at the very end of the movie. In the first movie, the character of Elizabeth Swann was written as a caring, kind-hearted, damsel in distress who slowly transforms into a tough pirate capable of taking care of herself by the events of this movie. A perfectly normal and necessary character progression that takes an abrupt turn when she decides to make out with Jack Sparrow to trick him into being chained to the doomed ship so the rest of the group has a chance to escape the Kraken.
Perhaps this is more of a personal opinion, but this goes against everything Keira Knightley's character had been portrayed to be at this point, for the sake of a plot twist that ends with Sparrow's death as well as tension with Will Turner that is able to last well into the next film as well. When a character makes such a departure from how they've previously been portrayed, it can theoretically still work. But in this case, the fault lies with the poor writing. This was so out of character, based on what we knew about her to that point, that it's extremely tough to believe that she'd actually do something like that. This inconsistency is more than enough to qualify this is as a plot hole.
2) The Avengers. Although it doesn't concern itself with being grounded in reality (making it easier to forgive things like Black Widow jumping onto a fast-moving Chitauri 'sled' and somehow not ripping her arm out of the socket), a few plot points are much harder to overlook.
For example, the fight in the forest between Thor, Iron Man, and Captain America. Loki had just been captured and taken by Thor before Iron Man interrupted and inexplicably focused more on fighting Thor than dealing with re-capturing the supervillain. On top of that, Loki just idly sits around and watches the entire fight take place rather than even pretending to escape.
Obviously his plan all along was to be caught, and the heroes even suspect something is suspicious. But to make it so blatantly obvious and the only response the Avengers have is a vague comment about it being "too easy" is a grievous oversight big enough to be called a plot hole.
3) The Matrix. Now, with such a sci-fi heavy story, it's important to take note of the 'rules' of the world it takes place in and go off that.
When it's first revealed that Cypher is a traitor to the main characters, we are shown that he is plugged into the Matrix having a nice fine dinner with Agent Smith. This is all well and good, but it's already been established that an operator (such as Tank) needs to be present in order to manually plug someone into the Matrix. Cypher chooses a time when everyone else is sleeping so that he can rendezvous with Smith and go over the terms for turning over Morpheus, so who exactly plugged him in?
It's fair to assume that any attempts at tricking someone into plugging him in at such an hour would immediately raise suspicions, and he obviously didn't force or threaten anyone because he takes part in rescuing Morpheus soon after this and no one raises any concerns. This is an instance where there may be a few possible answers, but none really work well at all. Thus creating a plot hole.
Hopefully these examples will put to rest the annoying tendency of misusing the phrase "plot holes" in some people's efforts to prove one movie or studio as a whole is better than another. Analyzing movies is fun, but nitpicking in desperate attempts to appear smarter than the general movie-going public is childish. Agree or disagree with my points? Sound off below!
** While writing this, I came across an extremely interesting article by a passionate and knowledgeable movie analyst known as the Film Crit Hulk. His strange pen name fits his equally unusual writing style, but his articles are well-written and incredibly thought provoking, for those curious. I have no other connection to him other than the fact it was a huge influence on me writing this article. Well worth a look!
http://badassdigest.com/2012/10/30/film-crit-hulk-smash-hulk-vs.-plot-holes-and-movie-logic/
and for the rest of his articles:
http://filmcrithulk.wordpress.com/