These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Complete Monster : The aliens. The President manages to see into their minds, and realizes that they have beem traveling across the universe, conquering and strip-mining all the planets in their path. It's at this point that he concludes that peace is impossible and declares that they should "nuke the bastards".
Hiller: You know, this was supposed to be my weekend off. But nooooo... Instead, you got me out here dragging yo' heavy ass through the burnin' desert... wit' yo' dreadlocks stickin' out the back of my parachute... You had to come down here with an attitude, packin' all big and bad...(pauses) and WHAT THE HELL IS THAT SMELL? (repeatedly kicks unconscious alien while screaming in frustration) I COULDA' BEEN AT A BARBECUE! (grabs parachute, continues dragging) But I ain't mad.
Not to mention Hiller and David's banter during the escape flight:
David: We're hit! We took a hit!
Hiller: We're not hit! We're not hit! Stop side-seat driving!
David: No! No! Tunnel! Tunnel! Left! EXIT!
Hiller: Where the hell do you think I'm going?!
David: No, they're closing on us!
Hiller: Shut up shut up shut up!
David: Faster, must go faster. Faster would be better! GO GO GO GO!
Hiller: (piloting the ship through just as the doors close) AAAAAAAAHHH! ELVIS HAS LEFT THE BUILDING!
David: No, no, thank you very much. I love you, man.
A Los Angeles news broadcast warns the viewers not to shoot at the spaceship: "You may inadvertently trigger an interstellar war."
Fridge Horror: The aliens take out NORAD. Isn't NORAD under a mountain?
Fridge Brilliance: The aliens have a Wave Motion Gun powerful enough to take out cities in one blast. So a mountain's not much of a problem.
David tells Marty to get his mother out of town. Marty tells her to go to her sister in Atlanta...which is later mentioned as one of the cities taken out in the second wave of attacks.
Harsher in Hindsight: Thanks to the now disturbing images of the destruction of the Empire State Building and the White House, this movie wasn't aired for a long time after 9/11.
Particular the image of the shadow crossing over the Twin Towers.
Money Making Shot: The alien ship blasting the White House is the emblematic shot of the movie. After that, it's the shadows falling over major landmarks, and their destruction that was the basis of the trailers.
Moral Event Horizon: The aliens' blowing up several cities at once is terrible, but what truly cements the aliens' status as unforgivable, especially in-universe, is when the captive alien reveals that they want to annihilate humanity, and they have done this to countless other worlds.
Snark Bait: Despite how much of a financial success this film was (with a worldwide gross of $816,969,268, the second-highest gross for a movie of all time back when it was released), the film attracts plenty of snarkers - especially non-American snarkers, who typically don't take kindly to America Saving The Day.
So Bad, It's Good: You can't not laugh at this movie, not to mention all the corny lines (the President's speech takes the cake in that department).
Strawman Has a Point: Nimziki gets two. We're supposed to be against his suggestion of using nuclear weapons but considering what we've seen so far that would be closest thing to a reasonable chance of success. Later he's supposed to be showing incompetence and cowardice for being against the plan to infect the mothership but the plan relies on a lot of luck, a human pilot managing to use an alien vessel, the aliens not getting suspicious and if it failed it would probably mean the end of all organized human resistance.
The look on Hiller's face when he finds out that the air base where his fiancee and stepson were headed has been destroyed. They're alive, but he doesn't know that, and they have a similar reaction when they think he's been killed.
Toy Ship: The President's daughter and Hiller's stepson
Visual Effects of Awesome: It still holds up well and the scope of the movie is awe inspiring. The sense of size and scale has not been matched by any movie since.
Woolseyism: Will Smith's "Elvis has left the building!" was changed to "Last train to Mikkeli has just left!" in the Finnish DVD.
Fridge Brilliance: The Roswell crash was a ship belonging to the movie's aliens. It was held in Area 51 since the 50s. Part of the conspiracy theory mythology involving the supposed aliens and alien technology at Area 51 (and possibly mentioned in the movie, it's been a while) is that a lot of modern technology was reverse-engineered from the alien technology in the ship. Put all this together, and it no longer seems quite so unreasonable that David could hack into the alien mothership with his laptop; it was probably reverse-engineered from the alien ship in the first place.
Similarly this shows that they have been doing Recon on the Human Race and America in particular for some time... this is presumably why the attacked when they did. Remember the comment that 40% of American soldiers are either on shore leave for the holidays or massed in Washington for the 4th of July parade? The Aliens knew that they were both unprepared and there would be a significant portion in DC so they could take a large part of their military leadership in one fell swoop. This is also why they targeted the White House.
It could also serve to explain why Captain Hiller can fly the alien ship. Every sub-sequent fighter-jet which came after the ship crashed was probably based on its technology in some way, shape or form.