Air Force One: The President's F/A-18 fighter is designated "Eagle One", but technically any USAF airplane that is carying the POTUS is automatically designated "Air Force One". Even if the President himself is piloting it and dogfighting aliens. If, however, it was a Marine jet, then technically it should have been "Marine One". Then again, Whitmore is the President.... Not to mention, after the rousing speech, he basically says that at that point, he's just a fighter pilot not the president because they need those more right now. Also, directly communicating during combat with a fighter identifying itself as carrying the President is probably not a good idea - the entire alien fleet, if they knew what "Air Force One" meant, would start targeting his jet.
Also, Air Force One becomes the de facto capital of the United States for a portion of the movie, as the President oversees the first counterstrike operation from aboard the plane. After that, Area 51 apparently becomes the de facto capital.
A Helicopter, presumably Marine One, takes the President away from the White House
Alien Abduction: Russell... or so he claims. The viewer is left to draw their own conclusions about whether or not this was entirely a delusion brought on by alcoholism, war trauma, or just being nuts. The novelization has him see the alien downed by Captain Hiller, and think that's it's not the same as the ones who abducted him. Then he starts to wonder whether other aliens are visiting Earth, or if it even really happened. The same novelization strongly implies that it did happen: inside their bio-suits, the invading aliens look exactly like the ones in Russell's memories.
There was a Marvel comic book that shows several events from the earlier lives of the characters, as a sort of "prequel". Russell is clearly shown to be abducted by the invaders.
America Saves the Day: And how. The entire plan to save the world was conceived by the American characters at Area 51, then broadcast via Morse code to the rest of the world. It's a Justified Trope, though, considering Area 51 is portrayed in the film as harboring a recovered scout craft used by the very alien race invading — implying that the U.S. has had decades to study them for forty years prior. Without that ace up its sleeve, the United States was as helpless as everyone else.
The producers of a British radio spinoff were even given strict instructions not to portray the British as in any way contributing to America's victory, likely as a pre-emptive move due to fears that perceived British distaste for the US military and distaste for this trope in general would lead the producers to attempt to downplay the US role in the victory strategy. Amusingly, the British radio version hangs a lampshade on this by having one of the characters remark, "What do you want to bet the Americans take all the credit for this?"
Anal Probing: Russell attests to having been abducted by aliens. Those who don't believe him crack jokes and ask if he was ever sexually abused on the flying saucer, suggesting this trope.
Apathetic Citizens: The few patronizing the strip club while an alien spaceship hovers over their city.
On the other hand, they're not paying attention to the strippers, but the TV showing the alien ships.
Everyone makes fun of Russell for believing that he was abducted by aliens, even after the aliens show up. But it's doubtful that his acquaintances got an opportunity to compare his description of the aliens to the one taken prisoner by Captain Hiller, and in any case, he's the town drunk.
Even after the attacks, the President refuses to believe in Area51, though in this regards, his disbelief stems from not being told it existed. As the leader of the nation, he assumed that something of such magnitude wouldn't have been kept from him — especially when aliens began arriving under his watch. It's pretty much the Secretary of Defense's fault for not informing him.
Area 51: Really is the site of a crash-landed flying saucer.
More accurately, the crash took place in Roswell, New Mexico, and the remains of the saucer — and its crew — were brought to Area 51.
Armor Is Useless: The aliens have biomechanical armor, but it doesn't seem to help them very much from being punched out. The armor might have helped against being shot, if Dr. Okun and the other scientists hadn't cracked it open to vivisect the alien inside. When Major Mitchell and the other soldiers shot it, its armor is open.
May be a case of Reality Is Unrealistic. Okun says that aside from their technology, the aliens are quite like us biologically. Even if a human has their head armored, a sharp, sudden impact can still knock them out, because it's the motion and impact that does it rather than any actual damage. Considering the alien had also just been in a high-speed crash, it being knocked out by Hiller despite its armor isn't far-fetched at all.
Artistic License - Gun Safety: Besides the infamous case of firing at the ship's deflector shield, at one point a marine receives orders while pointing his pistol at his superior with his finger on the trigger.
Artistic License - Physics: The gravitational pull of both the attack ships and the mothership would be enormous, and yet has no effect. And the less said of the advancing wallof fire that goes on through the tunnel without entering the room Jasmine is hidden, the better.
Authority Equals Ass Kicking: The President was a fighter pilot and leads a raid against one of the ships, though he doesn't get the final shot to take them down.
Benevolent Boss: Marty (Harvey Fierstein), David's Camp Gay boss at the satellite TV company. His immediate reaction when David warns him of the potential danger is to tell everyone to stop work and get to safety now. This is a media company that is covering the event: shutting off transmission long before others even guess of any danger would cost them $millions.
Big Damn Heroes: "It's me, Russell Casse, sir! Told you I wouldn't let you down!"
Big Entrance: Referenced. "You know me." "Yeah, I know, you always like to make a big entrance."
Bikini Bar: Jasmine is named as a stripper in dialogue, but we only ever see her in one of these. Justified as when we see her go into her routine, she notices no one is interested due to the invasion.
Bilingual Bonus: Julius Levinson (father of David), who had heretofore not been "on speaking terms with" God, is seen leading a group in the sixteenth benediction of the Shemoneh Esrei near the film's climax.
Bittersweet Ending: The aliens are defeated, but millions (if not billions) of people are dead, most of Earth's cities are in ruins, not to mention almost every military has been destroyed. The city destroyers falling to the ground will no doubt cause some further damage on impact.
Black and White Morality: The Earthlings defend their home planet against the evil, heartless galactic locusts from outer space.
Black Best Friend: A rare inversion. One of the main heroes is black and his white best friend (played by Harry Connick Jr.) is the wise-cracking comic relief. He fulfills almost every trope related to the black best friend, right down to being one of the first named characters to die.
Blown Across the Room: When the captured alien breaks loose in the Area 51 laboratory, several guards open fire on it through a glass window. When the bullets hit the alien it's blown backward across the laboratory.
Although, David does immediately point out that it's a bit unbelievable that Hiller is capable of flying the spaceship. Hiller retorts that David's virus plan sounds just as unlikely.
Of course, after decades of studying and reverse engineering the ship, the Area 51 scientists already know what the ships controls do, as they're all labeled (except for one that was backwards), so knowing how to operate the ship isn't much of an issue. Hiller's advantage is that he's the only human who's seen how well they're capable of maneuvering in various situations and lived to make use of that knowledge.
Calling Your Attacks: "Eagle Twenty, Fox Two!" And for good reason. Pilots call "Fox" one through four to indicate firing of different weapons to help avoid friendlies catching one of them. At least that's what these guys say, anyway. Plus it's all dramatic and stuff. In reality, with such a massive fleet of friendlies, this wouldn't be occurring at the outset since the radio feed would get garbled by fifty pilots doing their call while firing a simultaneous opening shot.
Fox calls are for air-to-air weapons, with the number indicating what type of guidance the weapon has. The Hornets in the final battle are carrying Harpoon air-to-surface missiles and should be making "Rifle" calls instead of "Fox" calls; "Fox Two" is only correctly used for heat-seeking Sidewinders, which are only used in the 'running out of missiles' part of the battle.
Captured Super Entity: At one point, Hiller captures an alien that crashed along with him and drags it to Area 51. The alien's telepathy and bio-mechanical suit make it a formidable force when it's found to still be alive.
Quite a few people David initially tries to warn about the alien "countdown" don't take him seriously, including his own ex-wife, who thinks he's either crazy or trying to get back at her for choosing her career over their marriage. However, his boss believes him immediately, and when he manages to meet with the President, Whitmore immediately takes his warnings seriously as well.
When Julius brings up Area 51, the Roswell Incident, and other alien conspiracies, the President dismisses it. It turns out Julius was entirely correct - the President just didn't know about it because the Secretary of Defense never saw fit to tell him (or, apparently, the Joint Chiefs of Staff) in the name of Plausible Deniability.
Russell Casse is a better example. Nobody believes that he was abducted by aliens, and thanks to his less than stable behavior, nobody takes him seriously when he warns that the alien ships are an invasion force.
Chekhov's Gun: When Russell gets inside his new fighter jet, he starts screwing around with the controls and accidentally arms a missile to be fired. Guess which missile jams at the end, forcing Russell into a heroic sacrifice?
A quick mention is made that President Whitmore is a former fighter pilot.
Similarly, a television reporter mentions in passing that much of the current information that anybody has is being passed around via amateur radio operators, given the widespread destruction of the government-run infrastructuresnote Which is actually a role that amateur radio fills in Real Life. Guess how the remaining military forces pass word to each other to coordinate their final counter-attack?
Chess Motifs: "And when the countdown reaches zero, then what?" "...Checkmate!"
The only man who figures out the alien signal is a countdown happens to have an ex-wife who works for the President, thus getting him access.
Hiller's girlfriend in Los Angeles happens upon the First Lady, so when Hiller finds her, he finds the President's wife (who everyone had pretty much given up for dead).
Hiller's dogfight with the alien fighter happens to take him near enough to spot Area 51, and his crash put him close to a convoy of refugees he can point in that direction.
A surprisingly large number of civilians amongst those refugees turn out to be former jet-qualified combat pilots. Although the recruiter specifically says while he is hoping for people with military training, "anyone who can fly a plane would be useful". The novelization takes it a step further, mentioning that they only have so many missiles to load on the jets, and some of them, with the least-experienced pilots, are going up completely unarmed to act as decoys.
Delayed Explosion: Almost every explosion in the film. The most notable is the explosion of Los Angeles, which apparently moves so slowly that Jasmine has time to grab her son, break open a locked maintenance closet, and even call her dog inside before the explosion reaches her location. It also, miraculously, does not fill the open closet with fire and debris. Nor does it suck the oxygen out of the tiny space, despite the fact the "sucking oxygen" would be the primary cause of the fire shooting through the tunnel.
Both issues are mentioned in the novelization: it spends a whole paragraph describing the Mind Screw effect of seeing an inescapable wall of fire slowly advancing towards you, and another paragraph to explain why Jasmine, Dylan and Boomer weren't deep-fried contrary to all those who hid in cellars (though the explanation is a bit shaky).
Deus Ex Nukina: You can destroy the unshielded atmospheric city destroyers and fighters, but the aliens have billions of reserves on board a super mothership in orbit. The heroes have exactly one trans-orbit Space Fighter; the enemy undoubtedly has thousands just like it, and they're more skilled at flying them. Fortunately it's already going to the mothership to enable the main attack—so the heroes load it with a single "tactical nuclear missile" to cause as much damage as possible. Instead, the entire mothership blows up.
Does This Remind You of Anything?: When Jimmy bends down on the floor to retrieve a wedding ring dropped by Hiller, another Marine passing by thinks he's proposing to his best friend. The other guy helpfully leaves immediately, not wanting to spoil the moment (or not wanting to get his friends kicked out of the military in the "don't ask, don't tell" era).
Dying Moment of Awesome: Russell Casse, who gets his revenge on the aliens by suicide bombing the destruction laser with an F-16 before it can fire. "Hello boys! I'm baaaaaaaack!" Taken Up to Eleven in the novelization - he flies his old biplane with a missile strapped to it.
The spoiled scene was filmed for the movie, but rejected as being too silly, even in the special edition. It also doesn't let the audience see Russell make the decision that the only way to save his children (not to mention the entire human race, potentially) is to sacrifice himself.
Earth Is a Battlefield: Featuring some pretty impressive set pieces when the humans fight over recognizable landmarks.
Earth Is the Center of the Universe: Not completely straight, but somehow the Earthlings managed to stop the alien advance when they've stripped who knows how many planets before them.
Easily Thwarted Alien Invasion: It takes a simple computer virus (and, y'know, a large nuclear warhead) to take down spaceships 1/4th the size of the moon and kill millions of aliens. Gotta love that universal Operating System!
Emergency Presidential Address: The President delivers an address to urge caution to the public as the alien ships enter the Earth's atmosphere and approach major cities. This is later followed by his "We will not go quietly into the night" speech once the aliens plans are revealed.
Enemy Mine: Israeli, Egyptian, Iraqi and English air forces are shown working alongside each other during the scene where the global counter-offensive is planned, seemingly having agreed to a mutual détente in the face of the alien threat. They also mention a Belgian contingent which was lost in the Sinai Peninsula.
Eureka Moment: David's idea to create a computer virus, coming from a simple reminder by his father to take care of himself lest he catch cold.
Every Helicopter Is A Huey: Though most of the aircraft used are period- and setting-appropriate, a Huey still shows up to escort the doomed S-64 Skycrane "Welcome Wagon". It explodes moments later.
Everyone Knows Morse: Except aliens apparently. Although they seemed to break the code pretty quick: first thing they did after the message was to send a Wave Motion Gun to Area 51.
They don't even need to read the message to deduce that a sudden rise in communications from a previously silent location means the enemy has activated a backup command center.
Eye Awaken: When the alien is being removed from its bio-mechanical suit. Major Mitchell later puts a few more bullets in it until it finally gives out a death cry, obviously aware of the trope.
Five Rounds Rapid: An initial assault with conventional weapons ends in a massacre as the Deflector Shield prevents their weapons from piercing the ships. However, once the forcefields are dealt with, they are susceptible to conventional weapons in their weak spot.
Flying Saucer: Played perfectly straight. And for once, actually scary instead of cheesy.
Four-Star Badass: General Grey, as contrast to the mousy, ass-covering Secretary of Defense Nimziki. Honestly, Gen. Grey's pretty much the only person in the government who manages to keep a cool head throughout the crisis, besides President Whitmore, who himself is a badass from the Gulf War. It's really no surprise that in the movie's second act — by which point the Vice President has been killed off-screen by the alien invaders — General Grey becomes the President's de facto second-in-command and closest adviser. It's likely that in the movie's universe, General Grey emerges from the crisis with a George Marshall or Dwight Eisenhower-like level of respect, and it's likely that he's either going to be Whitmore's new VP or Secretary of Defense... and the most likely candidate to be Whitmore's immediate successor once his term of office is up.
Frontline General: The Commander-in-Chief personally leads the final battle against the aliens.
Gatling Good: The F/A-18's feature a 20mm Vulcan cannon mounted in the nose. The fighters fall back on this weapon after their missiles are used up.
Genre Savvy: The characters figure out what the Deflector Shield does just from being aware of them from science fiction. Hiller declares "they must have some kind of protective shield over the hull". Yes, he picked the term "shield" which matches the sci-fi standard, but there's easily enough context for the non-savvy to understand just fine.
Gilligan Cut: The president says to leave the cities in an orderly fashion — cut to anarchy in the streets.
Guilt-Free Extermination War: The aliens, in keeping with their Horde of Alien Locusts nature, have no issues wiping out entire cities full of people. Humanity has no issues returning the favor for the alien mother ship. The US President actually does probe for peace even after they destroy every major city on Earth, with an alien that had just slaughtered a team of scientists no less; the response was a Mind Rape that would have killed him if the alien wasn't shot, and it showed him that their entire civilization is based upon this, moving from one world to another, wiping out the natives, using up all the resources, and then moving on to the next planet to repeat.
Since the skull is obviously human, it would probably be more shocking. Humans posed about zero threat to them up to that point.
Hemisphere Bias: Pretty much anything South of the Equator isn't worth concern. Though we get to see crashed UFOs in Sydney and right against Mount Kilimanjaro in Tanzania. There's even a news report with the subtitle "Southern Hemisphere Unaffected" under a map showing where the city killers are appearing (do note that the Southern Hemisphere is home to one of the ten biggest cities in the world - São Paulo, in Brazil — so in the context it's a wonder that the aliens have passed it up). Possibly justified, in that the aliens initially seem to be targeting the Earth's major military and industrial nation-states.
Not quite as severe as normal uses of this trope, but it was made quite clear that Jeff Goldblum's character was not too happy about the circumstances of what happened, eventually causing him to lash out, even litter the whole place quite violently before his dad inadvertently gives him an idea on how to defeat the aliens.
The President has one, lamenting of all the death and destruction caused by his indecision to prepare if the aliens indeed turned out to be hostile.
President Whitmore: We could have evacuated the cities hours ago!
First, the aliens' signal, that they used to synchronize their attack on the planet provided humans with a way to interface and access their systems (it's stated in the expanded edition that the same frequency is used for their communications) using a Mac of all things.
Second, the "Hammer". This is a nice one: If you look at the L.A. destruction scene, you'll see that the beam turns into a chain-reaction/explosion the moment it hits solid matter, and just keeps going until there's no significant obstacle left. Therefore, the denser the target, the worse the explosion (like the Mothership from Command & Conquer 3, which was inspired by this movie), making it perfect for leveling cities. When Russell crashed his plane into the generator, he did it at the very moment the beam started, and at the very "tip" of the gun, therefore setting off the chain reaction inside the alien's ship (which is likely to be just as densely packed as a city, if not more so).
I Come in Peace: Used straight and subverted. The military sends a chopper to one of the huge spaceships with a lit sign displaying greetings in all the languages of the world, and civilians in every major city hold up signs of greetings to said ships. The chopper gets blown out of the sky, and the cities (and associated welcoming parties) get cratered, with very little discussion. Later on, one of the aliens, through Dr. Okun, says, "No peace."
If I Do Not Return: When Casse realizes he has the only missile left and it's jammed, he says, "Tell my children... I love them very much," and flies his plane into the alien ship's weak point.
Ignored Expert: When the the City Destroyers arrive, it's a toss-up: many people are trying to get out of the city, but there's still a great deal of people who are partying and trying to greet the aliens.
I Got You Covered: At the end of the film, the President orders the rest of the fleet to cover Casse since he has the only missile left.
Immune to Bullets: The aliens, until you disable their force fields, take them out of their ships, and strip off their bio-mechanical suits.
Improbable Cover: Pretty much every time there's an explosion that the heroes escape, they do so by this trope.
Infant Immortality: Played straight for all of the named kids. Completely averted for several million other kids, some of which are seen being carried away by their panicked parents during the city destruction scenes.
Inscrutable Aliens: The aliens just show up and blow up cities, the only time they communicate with humans is when one is taken prisoner and takes telepathic control of a scientist in order to demand its release.
In Working Order: The crashed alien ship from Roswell still works. To be fair, though, they have quite obviously patched huge sections of the hull with Earth-made metal plates, and they've had decades to work on it.
"Checkmate" takes this to ridiculously lampshaded lengths.
And the First Lady lovingly calling her husband "Liar."
Right before the attack begins, David realizes that the strange signal the aliens are using is a count-down to attack. The virus at the end gives David the chance to do the same to the mothership, doing a count-down to the nuclear explosion that takes the ship out.
Israelis with Infrared Missiles: The Israeli military appears in a brief scene and is more than capable of taking out the alien ship in its part of the world. It's also an Enemy Mine scene as it shows they have set up camp inside Iraq alongside British and Iraqi forces.
It Has Been an Honor: Hiller and David have a moment of this at the end of the film when it appears they're not going to survive bombing the alien mothership.
The F/A-18C is shown to have a deployable braking parachute. The F/A-18, being a carrier based aircraft does not actually possess a braking parachute, relying on its arrestor hook to slow it down when landing on carriers. It is also shown being capable of maneuvering through a canyon, something it is definitely not able to do in a canyon of the size shown in the film.
The RAF (Royal Air Force) is shown operating F-16C Fighting Falcons, whilst the Israeli Air Force is shown operating F/A-18C Hornets. Neither air force has ever operated, or intends to operate those fighters.
Following the devastating alien attack, F-14 Tomcats are seen on the tarmac at MCAS El Toro. The F-14 is not operated by the Marine Corps, it is a Navy aircraft and is thus meant for carrier operations.
A B-2 Spirit stealth bomber is shown deploying a nuclear missile at close range to its target. The B-2's low speed and maneuverability would mean it wouldn't escape the ensuing blast and EMP. Realistically it would deploy its payload at BVR (Beyond Visual Range).
Match Cut/ Tempting Fate: One of the president's speeches, being witnessed in the deserted office building by Levinson and his boss, ends with a close-up of his face as he encourages the nation "If you feel the need to evacuate, please do so in an orderly fashion". Cue mass pandemonium in the streets, riots and looting spreading like wildfire.
Meaningful Name: Russ T. Casse. (That would be "Rusty Case" if you didn't know).
Missing Mom: David Levinson. The Casse kids. The President's daughter, presumably, after the events of the movie.
Mistaken for Gay: Hiller's wingman gets down on one knee to demonstrate how to properly kiss ass, and then a wedding ring box falls out of Hiller's locker. When he shows it to Hiller, another pilot walks by, sees the scene and quickly excuses himself. "Don't ask, don't tell," of course.
Steven: Is it an earthquake? Jasmine: Not even a four-pointer, go back to sleep.
Monumental Damage: It's taken to an extreme, which shouldn't be surprising since this is a Roland Emmerich film. Amongst the casualties are the Empire State Building, the White House, The Capitol Records Building and the pyramids of Giza. The trailers spoiled this one big-time. The first thing you see is the decapitated head of the Statue of Liberty, after the alien attack.
Mood Whiplash: Hiller's line that he's always dreamed of flying in space accompanied with majestic music and the image of the craft flying triumphantly away from Earth... only for the music to suddenly turn dark and ominous as the camera pans to show them heading towards the Mothership.
When the President orders his men in the final battle to "Plow the Road". Although, for F/A-18s, that was actually quite insufficient Dakka. The Vulcan Cannons carried by American fighter jets fire at a rate of about 6,000 rounds per minute in Real Life.
Also in Real Life, the F/A-18 only carries 578 rounds. There's a reason its only mode is burst fire.
No Endor Holocaust: Dozens of ships that size hitting the ground would throw up enough dust to blot out the sun. And that's not even considering blowing up something as big as the mothership in Earth's orbit like that.
The novelization mitigates a bit by putting the Moon between the Earth and the mothership. This makes sense if you consider that something that big would have to have a huge angular velocity to maintain Low Earth Orbit. However, the movie shows an enormous amount of debris racing the delivery fighter back into the atmosphere, and later burning as "fireworks" overhead. If it was actually out beyond the moon when it detonated, the number, implied velocity (a good chunk of the speed of light) and size of those fragments would have been a rather incredible bombardment all on their own.
When Will Smith takes the day off, he takes the day off.
No Sell: The aliens' force fields are effectively impenetrable as far as earth's defensive forces are concerned. At one point, they shrug off a direct nuclear attack. They seem to hardly notice counterattacks- until, that is, their shields are disabled, and then things start going the other way.
Nuclear Option: Nuclear weapons are used only once, over Houston (a city that's about to fall victim to one of the leviathans), and after significant consideration (primarily over the fact that, whether it works or not, the city is about to get razed to the ground anyway). When the first one doesn't work (read: didn't even get through the target's shields), the rest are immediately called off.
Darker and Edgier in the novelization: this is only briefly mentioned in the movie, but not only is Houston still completely intact at the time of the attack, it hasn't been fully evacuated yet.
Of course the only other nuke is used in a "safer" context without human casualties, detonating from within the mothership after Hiller and Dave bring it inside.
Obstructive Bureaucrat: Secretary of Defense Albert Nimziki. Before he became the Secretary of Defense job he was the CIA Director. They had evidence of a hostile alien race, they KNEW what they were capable of, and yet they DIDN'T. TELL. THE GOVERNMENT. This results in the initial counterattack against the aliens being utterly annihilated due to the shields and the US losing hundreds of pilots that could have been more useful if they actually had a way to beat them. The guy eventually tries to talk Whitmore out of attacking the aliens before the end battle, claiming it would be a mistake. Whitmore replies:
Whitmore: The only mistake I made was appointing a sniveling little weasel like you as my Secretary of Defense. Fortunately, that's a mistake I'm glad to say that I don't have to live with. Mr. Nimziki... you're fired.
Although to be fair, they didn't that know that much about the aliens other than what the crashed craft had brought with it. They didn't know what to expect in terms of weaponry and defensive systems.
It's hard to read expressions on an alien face but it's easy to imagine that's what it was thinking when it found itself staring at a countdown on a nuclear missile that just ticked to zero...
These are Harvey Fierstein's character's last words.
An amusing example occurs when Steven Hiller is reading the paper on his front lawn. He looks left and right, bewildered at all his neighbors apparently moving out at once. Then he looks straight ahead and sees the miles-wide spacecraft hovering over the city.
The Air Force flies out to engage one of the giant flying saucers, they fire their missiles at it, and... the missiles hit a Deflector Shield.
The president finally authorizes the use of nuclear weapons, a B-2 bomber launches a Tomahawk cruise missile at a giant flying saucer while it's over an evacuated city, the bomb explodes, the air clears, and... the flying saucer is undamaged.
Connie asks Major Mitchell what happens if the aliens get there before they plant the computer virus. He mentions that the mountain should afford them some protection. She then asks him about the people on the surface. Aahh.
They've finally brought down the flying saucer's shields, they're hammering away at it with missiles that just aren't taking big enough chunks out of it, and then, right when it's over their base... it opens its city-incinerating gun port. The background music at this moment plays the most Oh Crap-ified version of the alien motif in the movie.
Whitmore: DOESN'T ANYONE HAVE ANY MISSILES LEFT?! Russell: Sorry I'm late, Mister President!
Organic Technology: The alien's suits are more like a second organism that they ride inside of. Word of God states that most of their technology is at least partly biological as well.
Word of God isn't even really needed — Okun specifically states that the suits are "biomechanical", indicating that the suits are either fully organic technology, or a mix of organic and manufactured technology. In fact, the whole design aesthetic of the alien race implies that biology is a major influence on their "look".
Planet Looters: "I saw... his thoughts. I saw what they're planning to do. They're like locusts. They're moving from planet to planet, their whole civilization. After they've consumed every natural resource, they move on. And we're next."
Planet Spaceship: The alien mothership was estimated to be several hundred kilometers in diameter, or nearly a quarter the size of Earth's (very large) moon.
Plausible Deniability: Played straight and directly mentioned, as the Secretary of Defense kept the President in the dark, and also the Chairman of the Joint Chiefs of Staff by judging his reaction to learning this.
President Whitmore: My God... Why wasn't I told about this place?
President Whitmore: I don't understand, where does all this come from? How do you get funding for something like this? Julius Levinson: You don't actually think they'd spend $20,000 on a hammer, $30,000 on a toilet seat, do you?
Fridge Brilliance: The scientists at Area 51 had been studying the craft for years. Odds are they had some idea of how its systems work. (Granted one scientist states things switched on since the invaders arrived. This has no qualifiers, however, for if the ship runs on electricity, there is no reason the scientists couldn't jury-rig a generator to run parts of the ship during their research.) If the scientists knew the basics of how the aliens' computers operate, they could write a virus for them. What if they are not compatible? Fridge Brilliance covers this as well. If they know how the software works they could write an emulator to operate on a terrestrial computer for the specific task of uploading the virus. This would even explain the Hollywood Hacking where a window pops up saying "Uploading Virus" rather than a more generic "Uploading File".
Power Armor: Bio-Mechanical in nature, and offers little protection from a punch to the face (which doesn't actually line up with the real head), but with several built-in weapons and decent protection from bullets.
Russell Casse, before he proceeds to shove his F/A-18 up the alien ship's ass and completely annihilate it in a glorious (and, for him, quite satisfying) Heroic Sacrifice.
Russell Casse: "Hello, boys! I'MBAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACK!!
The President moments prior: "All right, boys, let's give Mr. Casse some cover. GENTLEMEN! LET'S PLOWTHE ROAD!"
Deep in the mothership and not expecting to get out, Hiller makes a V-sign to the alien in charge of the hangar, shouts "PEACE!" and fires the nuke. And just beforehand, David activates a special option in his virus causing all the alien display screens to show an animated laughing skull and crossbones, complete with demonic-sounding digital laughter.
After the captured alien launches a mental assault on Whitmore and shows him their plans, we get this:
Grey: Is that glass bulletproof? Mitchell: No, sir. (all observing military personnel pull out handguns and open fire)
Product Placement: The best-known example is Jeff Goldblum using a PowerBook 5300 (ironically considered even by die-hard Apple fanboys to be one of the worst Macs ever made) to hack into the alien ship.
Random Smoking Scene: Will Smith's character and his comrade both take cigars along with them when they plan to defeat the aliens for once and for all. And they do smoke them after all the aliens are dead.
This seems to be standard for Capts. Hiller and Wilder as they both take cigars along without any prior conversation and they both take waiting until "the fat lady sings" to smoke it very seriously.
It appeared to be a tradition with the Black Knight squadron. They would take a cigar along on the flight and smoke it after a successful (and they are Marines so all are) missions. That's why when Hiller needed the cigars before he and David left to go deliver the package.
Hiller: Almost put a hex on the whole thing.
Reality Ensues: Once they figure a way to get around the alien force fields, they realize that they are still trying to take down city-sized spaceships with regular aircraft missiles. It isn't until they find the Achilles' Heel that they stood a chance short of nuclear weaponry.
Risking The King: President Whitmore takes up a fighter and leads the final battle against the aliens. Justified, as he's one of the few men around who can fly a plane (and has combat experience) and if they lose, he won't have a country to lead anyway.
Rock Beats Laser: Played with as the aliens used Earth's satellite system to coordinate their attack, giving David a chance to study their signal system and turn their own trick back on them.
Rousing Speech: "We will not go quietly into the night. We will not vanish, without a fight. We're going to live on. We're going to survive. Today... we celebrate... our Independence Day!"
Rule of Perception: Steven and later Jasmine walk out onto their front lawn with a view over Los Angeles and don't notice the alien ship hovering silently over the city — until the camera shows it.
Scare Chord - Two of these can be heard within the timespan of a few minutes.
The first one occurs when Dr. Brackish Okun and a few medical assistants at Area 51 are attempting to remove the biomechanical suit from the unconscious alien and it suddenly rips open.
The second one occurs after the alien wakes up, kills the medical assistants plus Dr. Okun, and destroys most of the containment laboratory. With most of the room in a dense fog, President Whitmore gets near the glass separating the rooms when Dr. Okun's lifeless body abruptly appears from out of the fog right up against the glass.
Scenery Gorn: This film revels in the wholesale destruction of the populated centres of the world. (Emmerich returned to make similarly spectacular carnage in The Day After Tomorrow and 2012). Love of this trope must be the reason that a movie which features the destruction of the White House is shown on American television every year on the Fourth of July.
Schizo Tech: For the aliens. They have the space travel, laser beams, indestructible forcefields... but their computer security technology is so primitive a guy with a laptop can hack it; they didn't even think about the possibility of a security breach, even though they were interfacing with the Earth's satellite network. It wouldn't be the first time an alien race of invaders had some technological deficiency that lead to them being defeated (it goes all the way back to War of the Worlds) but this one is particularly egregious.
The computer security thing could well be justified. Considering that they appear to be a monolithic hive culture, it's entirely logical that these aliens would have never created computer viruses of their own, and therefore never needed firewalls and anti-virus programs on their own world. Then, once they were out in space, they might never have encountered them until us. After all, most of their victims were probably less advanced than us, and even we win only due to a 'perfect storm' of circumstances, i.e. 1: We're advanced enough to have the concept of a virus program. 2: We're flexible-minded enough to conceive of using such in this way. 3: We're lucky enough to have a functional alien ship with which to carry out the attack.
Of course, you have to wonder how our primitive computers could interface with something so alien, let alone shut it down.
Semper Fi: Marines have a strong presence in the films cast. Will Smith is a cigar chomping Marine Corps F-18 pilot. William Grey, the President's most trusted right hand man throughout the film, is a Marine Corps General.
Grey is alluded to (if not outright referred to) as the President's former commander, which strongly suggests that President Whitmore is a Marine as well.
Shell-Shocked Veteran: The news report on Russell claims he got this as a result of being a fighter-pilot in Vietnam, but he claims it's from his abduction.
To Jurassic Park; Jeff Goldblum's character says, "Must go faster. Must go faster. Go, go, go, go, go, go, go, go!" in the same way as he does in one scene in Jurassic Park. Exactly the same way, in fact: the audio was cut directly from Jurassic Park and pasted into this movie.
There are also shout-outs and Easter Eggs to classic sci-fi shows and films dating all the way back to the 1940s. Most specific among these is the bomber sent to deliver the nuke - the Northrop B-2 Stealth bomber is the direct descendant of the Flying Wing tasked with the same mission in George Pal's version of War of the Worlds, which was a real Northrop XB-49 and not a Hollywood prop.
The strategy to defeat the aliens mirrors the defeat of the aliens in The War of the Worlds, with a different interpretation of the word "virus".
3001: The Final Odyssey (which came out the year after ID4; presumably Clarke had decided on or even penned the ending before ID4 came out) has the heroes dispatch the aliens with the exact same strategy. Arthur C. Clarke writes in the ending notes that he doesn't know "whether to congratulate them for their one stroke of originality or accuse them of retroactive plagiarism". (not exact quote)
Smart People Play Chess: Julius and David Levinson are shown playing chess together early on, with David winning easily. He spends much of the rest of the movie talking in Chess Motifs.
Some Kind of Force Field: When the first air-to-air missiles reveal a invisible barrier surrounding the big flying saucer, Hiller declares, "They must have some kind of protective shield over the hull!"
Sound to Screen Adaptation: Inverted with Independence Day UK, a BBC radio drama based on the movie, but set in the UK with original characters. The one stipulation Fox placed on the BBC was that the Brits couldn't substantially contribute to the Americans' victory. This leads to one character muttering, "I bet the Yanks are going to take all the credit!"
Swiss Cheese Security: The Area 51 guard lets Steven and his huge convoy into the base without so much as a phone call.
Taking You with Me: Russell gets revenge for his abduction years back and shows humanity how to win the war.
Steven and David fire the nuke as a last resort after being trapped in the mothership.
Telepathy / Telepathic Spacemen: The alien's natural means of communication. It also seems to work across species in a limited manner: the captured alien is able to control Dr. Okun's body to speak for it, and can even attack President Whitmore telepathically. Supplemental material states that the aliens are designed to reflect their telepathic ability, having their huge heads shaped a bit like antennae.
Television Geography: A few examples, the most blatant being the Empire State Building (which is located in the middle of a block in real life, and yet in the movie has a nearby street).
This Is Gonna Suck: David when the city destroyers show up and he realizes that the mysterious signal he found in the satellites is actually a countdown to a global alien attack.
Those Two Guys: David Levinson and Captain Hiller, neither are the most important person in any scene they are in, yet keep saving the day.
Also, the two USAF officers who work side-by-side from Air Force One to Area 51.
The people that were waiting to the aliens in the rooftop of a building in Los Angeles. Including Tiffany, who promised Jasmine she wouldn't. At first, these people had no explicit reason to believe the aliens were hostile, so they were more optimistic than foolish. It's only when they ignored police loudspeakers urging them to evacuate that they became idiots.
Also those "scientists" that were diagnosing the alien without any security nearby despite the fact that they knew the alien wanted to kill them.
While he doesn't show much stupidity anywhere else, David Levinson asking Major Mitchell to fire a bullet at the alien spaceship definitely qualifies. Has the man never heard of gun safety? The bullet ricochets dangerously around the room containing what's left of the American administration and the only scientists on Earth with knowledge of the aliens' technology. He's a scientist with either little or no knowledge of guns, and he probably assumed that the bullet would just flatten against the shields instead of ricocheting.
Too Fast to Stop: The alien dogfighters, inexplicably, towards the end of the movie, even though they are stated to be extremely maneuverable.
Trojan Horse: The alien fighter that crashed in Roswell (and the Area 51 scientists repurposed for humans to pilot) is used to invade the mothership (where Dave will shut down the forcefields and Hiller fire a nuke to destroy the thing from within).
Tropes Are Not Bad: There's a reason this movie spawned the "Big Willy Weekend" tradition.
Hiller claims that he is one of the few fully aware of the alien fighter capabilities and that being a pilot he can figure out how it works. Parodied in that his first attempt in the cockpit ends with him going in reverse. Although admittedly the controls seem fairly intuitive, using dual joysticks. The movement directions being labled wrong by the scientists wasn't helpful.
Lampshaded earlier, when David asks him quietly if he really believes he can fly it.
Becomes a bit of a Funny Aneurysm when you realize that was probably the missile that failed to fire, meaning he had to die instead of just firing it and going home to his kids.
The missile arms correctly, the malfunction is from the release mechanism and the ignition of the rocket won't start until it detaches. His problem is that he has a live missile up and no way to dump it except ramming it against the target. It would have happened even if he didn't arm it by mistake. That's why it's one of the few genuinely moving scenes in the movie: Russell knows there is only one way to deliver the payload and that it will take his life. Heroic Sacrifice played to the hilt and with a believable reason. Realistically though, the missile would just fire its motor and break free of the mechanism holding it to the plane.