The two films in the current franchise provide examples of:
Action Girl: Sue, of course. Also Cpt. Frankie Raye. (Nova from the comic books)
Actor Allusion: More "actor input", actually: Julian McMahon, who plays Dr Doom, suggested that metal staples be used to help stitch the scar at the beginning of his transformation. This comes from McMahon's experience playing a cosmetic surgeon on Nip/Tuck.
A God Am I: Victor starts thinking this way once he embraces his powers. Sue notes that he always thought of himself as above others, though.
Arbitrary Skepticism: Ben in the second movie is initially incredulous when Johnny claims to have seen a "Silver Surfer", despite the fact that most of the people in the room have superpowers and his body has been transformed into pure rock?!
All Your Powers Combined: Johnny at the end of the second movie. After being a screw up due to his unstable form for most of the movie he uses it to his advantage at the end.
Avoid The Dreaded G Rating: Surprisingly averted in the sequel. The director actually stated that he didn't want to pepper the film because he was happy with its PG rating. It helps that the FF's adventures and tone have almost always been rather family-friendly.
Badass Boast: Reed, and it was taken almost word-for-for from the Warren Ellis comic book:
General Hager: Let me make it clear for you and your band of freaks here; I'm the quarterback. You're on my team. Got it? but I guess you never played football in high school, did you, Richards?
Reed: No, you're right. I didn't. I stayed in and studied like a good little nerd. And fifteen years later, I'm one of the greatest minds of the 21st century; I'm engaged to the hottest girl on the planet; and the big jock who played quarterback in high school? He's standing in front of me asking for my help. And I say he's not gonna get a damn thing, unless he does exactly what I tell him, and starts treating me and my friends with a little respect.
Curb-Stomp Battle: Super-powered Johnny versus Doctor Doom in Rise. Doctor Doom acquires the Surfboard of the Silver Surfer- which allows him to fire stupidly powerful energy blasts- and to combat that, Johnny grabs the powers of the entire team to take him down. Doom never even gets a single shot off.
Deleted Scene: The DVD Extended Edition, which includes all deleted scenes (such as Ben and Alicia's romance) is a much better watch than the theatrical release.
Demoted to Extra: In the comics, Alica Masters (Ben's blind girlfriend) was the one who appealed to the Surfer's "humanity" and convinced him to save the world from Galactus. Here, Sue is given that job, and Alicia is only given two scenes in the sequel.
She only has two scenes in the first movie too, so while it's a demotion from the comics it's a pretty consistent (if minor) role in the films.
Disposable Superhero Maker: Played With; the cosmic storm is a once-in-millenia event but Reed manages to recreate it in his lab (yeah) and... well, we don't know what exactly he did with the machine, 'cause it's never revealed in the movie.
Distracted by the Sexy: Subverted. It looks for a second like Reed is staring at Sue in her skin-tight outfit; but then...
"Wow! Fantastic! Material made from self-regulating unstable molecules!"
Doing It for the Art: One of Chiklis' requirements for accepting the role of the Thing was that his character would be make-up based, rather than the CGI everyone else had previously assumed. This meant that Chiklis insisted upon hours of application and wearing heavy, uncomfortable makeup, over the option that would have allowed him to earn the same money in significantly less time simply by voice acting. Why? Because Chiklis was a fan who knew that underneath the rock skin, Ben Grimm's still a human being, and this was best shown by having his actor go through the same thing.
Dramatic Irony: The scene shot from Ben Grimm's POV, when he wakes up after being hit by the cosmic storm. Everyone watching the film knows he turns into the Thing, so when Johnny Storm says, "Everyone else is fine." we think we know what's wrong with Ben. Then it turns out that Johnny is making fun of Ben's human looks.
Johnny Storm: I'm sorry, but the doctors just couldn't do anything to fix your face.
Dysfunction Junction: At least in the comics they never came into actually trying to hurt each other...
Ioan Gruffudd is, in all seriousness, quite a dashing fellow and managed to bring a lot of charm to the character of Reed Richards. Especially the scene in the first film where he stretches his chin to parody Superman and/or Batman from the animated series.
Every Helicopter Is A Huey: In the sequel, as the team are flown over the Thames in a pair of Hueys. Since the US military long since phased out the Huey and the British military never used them at all, it's anyone's guess where on Earth they even got the things unless they raided an air museum.
Fakeout Escape: There's a sequence in Rise of the Silver Surfer (imported from the original comics) where Sue turns invisible when government officials come to check on her, then runs out the doorway during their confusion.
Genius Bruiser: One of the few versions where Ben Grimm (The Thing) is just as clever and savvy as you'd expect from a former test pilot and astronaut. Even Book Dumb is averted with him.
This is best seen in RotSS when Reed is given photos of a 'comet' (actually the Silver Surfer) that's entered the Earth's atmosphere. Reed immediately hands the photos to Ben, who points out that the object can't be a comet because "the trail's all wrong". A subtle but brilliant nod to Ben's astronaut career.
Getting Crap Past the Radar: In the sequel, when Sue gets the Human Torch's powers, her clothes burn off, which means for a short period of time, she was naked. But that also means she was naked while on fire, and you can clearly see her breasts bouncing about during that time.
How Do I Shot Web?: Reed and Ben don't have much difficulty figuring out their powers but Sue and Johnny have a some trouble with it at first. This is the rare franchise to manage this again in the sequel with the four struggling to use each other's powers.
Justified with Ben as his powers learning curve largely centre around controlling his own strength. Reed to a lesser degree as his mainly involves extending his reach and not any form of energy projection.
Idiot Ball: In Rise... General Hager... It's one thing when the military does not trust superheros. It is another thing when that same general agrees to work with the guy who is not only WORSE than what you believe, but also took all of the Fantastic Four to defeat him in the previous film. Nice judgement, Hager.
Incredibly Lame Pun: In the second film, when Surfer!Doom whips up a tornado for the Fantastic Four. "Let's all go...FOR A SPIN!!"
Invisible Streaker: In the first movie, Sue is forced to strip naked in the middle of a bridge because her clothes don't turn invisible along with her skin. A pretty egregious piece of fanservice, considering her powers were designed specifically to rectify this problem (she makes herself invisible by projecting forcefields that refract light, and should make everything within them invisible).
Lightning Bruiser: The Thing retains this status from his comic book version. No mean feat, considering Mike Chiklis is weighed down by several kilograms of makeup.
In the second movie the makup had improved to be lighter and allow Chiklis more freedom (in the first movie he couldn't even sit down while wearing the full costume and makeup). This means that he gets even faster and more dangerously agile in the sequel.
Logo Joke: The two movies—released by 20th Century Fox—featured the TCF logo segue into the page-flipping Marvel logo. The Marvel logo also has a logo joke of its own, featuring only Fantastic Four panels and making the background behind "MARVEL" blue (like the F4 outfits) instead of the traditional red. Sadly, the extended cut of the 2005 movie removes the segue between the logos.
Look Ma, No Plane!: In the second movie, the Human Torch flies next to the plane in which the rest of the Fantastic Four is flying, annoying the Thing.
Victor: I have four words. Four little words that can change our lives forever...
Reed: THE CLOUD IS ACCELERATING!
Ms. Fanservice: Sue. Or more accurately, Jessica Alba. Even more specifically, Jessica Alba in a skintight spandex jumpsuit. Lampshaded during the 2005 film. She also gets all her clothes burned off when she and Johnny switch powers in the sequel. In front of a whole load of people. At least in the first movie she still has her underwear. Which she has to take off so no one can follow her... Alba reports that her death scene in the second movie was reshot with the direction to die sexier. Made even more obvious since her power is to bend perceptions or something to that effect. Opinions vary whether her stripping it off is justified in-universe.
Mundane Utility: Johnny makes popcorn using his powers. Ben uses Thing-strength to squeeze orange juice. Reed uses his stretching to write on blackboards far away from him, and to retrieve toilet paper from another room. The Four's uniforms are modified from the underclothes they wore on the space station.
Mythology Gag: The Thing saying, "You know, I used to smoke." Also:
Johnny: That's the Invisible Girl!
Stan Lee's cameo doubles for this in the second movie; in the film, he was turned away from Reed and Sue's wedding, just as he (and Jack Kirby) were for the wedding in the comic.
Johnny getting the powers of all his teammates makes him very similar to FF nemesis Super Skrull. He even hits Doom with a stretchy rock covered flaming fist.
The Puppetmaster, Alicia's stepfather, is given a brief mention in one of the deleted scenes.
The cloud of Galactus features a brief shadow of his helmet as shown here◊
During an examination, Ben mentions that he used to smoke. The Thing used to smoke cigars in the comics, until Joe Quesada became editor-in-chief in the mid-nineties, and issued a mandate banning all images of smoking across all Marvel Comics publications.
In the extended version there's a scene (right before he's "cured" by Doom) of Ben on a bench with his hand to his mouth that makes it look like he's smoking. Turns out it's just cold.
Skunk Stripe: The movie shows how Reed got his, part cosmic radiation, part obsessive guilt over the accident that caused their powers.
Snow Means Cold: Subverted when the Surfer's passage causes snow to fall on the Great Sphinx outside Giza, Egypt ... without a corresponding drop in temperature.
Soft-Spoken Sadist: Victor. He only raises his voice once over the course of the two movies, during a point when he was more desperately angry than evil. Everywhere else it's smooth, softspoken sinister sliminess.
Technology Marches On: In the second movie Reed is shown using a very clunky looking ultraportable, a type of computer design that looked dated within a couple of years of the movie's release due to netbooks, smartphones, tablets and ultrabooks.
The Pirates Who Don't Do Anything: One of the most common criticisms of the first movie. Barring the final fight scene and a rescue scene in the middle (the latter being for an incident they caused, mind you), the Fantastic Four really don't do that much, well, fantastic stuff.
The Unreveal: First scene in the hospital after the radiation cloud hits, features Johnny sorrowfully explaining to Ben that the doctors did "everything humanly possible." Filmed entirely from Ben's point of view, audience is led to believe Ben's become the thing, only to discover that Johnny is just messing with him when he looks in a mirror. He changes a few scenes later.
It may have also been for the benefit of Alicia, who was standing right next to him,(she's blind).
In that case, why the "Aw, look" part, though.
Too Dumb to Live: In the second film, the General repeatedly trusts Doom over Richards, even giving him access to study the Surfer's board. He even has the audacity to appear surprised when Victor inevitably screws everyone over and steals the board for himself!
Unfortunate Implications: In-Universe example. Unlike the regular version has Reed grow a Lantern Jaw of Justice, the extended cut of this film has Reed Richards transform in to Wolverine when saying to Sue that he "thought [she] wanted a stronger man". This suggests that mutants exist at the time the movie takes place. I'm sure Johnny Storm's comments about Ben Grimm on public television ('every team needs a mascot'!) went over really well with the mutant community.
A CEO suggests that Doom 'go back to the home country,' and that maybe he belongs there. Usually the audience could just suspect that he was being the average Jerk Ass CEO. But then at the end of the movie, they actually pack him up in a storage container headed for Latveria while the American heroes celebrate their victory.
What Could Have Been: The 2005 film was originally meant to be, in executive producer Chris Columbus' words, "the most epic sitcom ever made", and they were consciously trying to duplicate the formula that had resulted in the utter failure of Batman & Robin — Columbus' reasoning being that while Batman wasn't an appropriate franchise to attempt such a formula, The Fantastic Four was. After a few years in Development Hell, the arrival of Tim Story (who, ironically, was mostly known as a comedy director) and writer Mark Frost finally pushed the film in the right direction.
This feel is best seen in the hilarious breakfast scene and the montage that follows it. The whole thing plays out like an hilarious cross of Leave It To Beaver and The Addams Family.
With Catlike Tread: In Rise of the Silver Surfer, they decide that the only way to get the Silver Surfer's board back from Dr. Doom is to use The Human Torch's new "powers" to combine all their abilities to allow him to fly, but also be as strong as The Thing, and be invisible so he can sneak up on Doom. It works perfectly and he gets to within 2 feet of Doom. But rather than just knock him out, he has to say "To quote a friend, It's clobbering time." thus blowing the cover and starting a drawn out battle..all while the Earth is about to be destroyed.
Well, Doom had just killed his sister.
Working With The Ex: In the first film, Reed and Sue had once dated and broken up, only to meet up again when Victor brings his chief genetics researcher (and girlfriend) along to the space station, causing some tension and old feelings to arise.