The Faceless: Sylar, for a surprisingly long time after he was introduced as a character. The first time we actually see his face is in a flashback; therefore the fact that he's uncomfortably handsome is more of a shock. This is, of course, due to the fact that the first part of Season 1 was filmed before Sylar was actually cast, with veteran voice actor Maurice LaMarche providing his voice in the Sylar/Chandra phone call and the on-set Sylar being played by stunt doubles until Zachary Quinto was hired.
Fake American: Matt Parkman's wife Janice is played by Australian Lisa Lackey.
Fake Brit: Adam is played by Oregon native David Anders.
Fake Guest Star: James Kyson Lee gets this treatment throughout Season 1, even though Ando appears in twenty-two out of twenty-three episodes. That's more than Peter, Nathan, or Mohinder, and way more than Simone.
Fake Irish: Samuel and Ricky are played by Americans Robert Knepper and Holt McCallany. Will and Caitlin are played by Brits Dominic Keating and Katie Carr.
Fake Nationality: See Fake Brit and Fake Irish above. James Kyson Lee (Korean) plays Ando (Japanese). Additionally, while Mohinder is from India, Sendhil Ramamurthy was born in Chicago and grew up in Texas. Lampshaded by Ando who says (of white people, though): "They all look alike."
Family Versus Career As a part of Samuel's plan to manipulate Hiro, he hides Charlie in 1944 Wisconsin. Since Charlie's power is perfect memory, and she had spent the 6 months prior to her appearance learning everything there is to know about everything, she's a walking Timeline-Altering MacGuffin. Despite being in a unique position to manipulate world events (or at very least make herself fantastically rich), she chooses instead to be Rosie the Riveter and raise kids.
Fandom Nod: Sylar explains that he, in fact, does NOT eat brains.
Also in one GN when meeting a trio of evolved humans who think of him as an inspiration, Sylar notes with some surprise "I have... fans!?" most likely a nod to the Sylar fandom.
Fantastic Aesop: There are episodes devoted to explaining that You Can't Fight Fate and/or change the past. This, however does not apply to the future. You can change that as much as you like. In fact the resolution for both the first and second Volumes is the characters preventing a future event, one witnessed firsthand by one or more characters, from happening. This seems to imply that the "present" timeline that most of the show takes place in is somehow more valid or real than any other timelines.
Fat and Skinny: Hiro and Ando are a downplayed version. Hiro is happy, idealistic, and a little on the short and chubby side, whereas Ando is much more worldly and is a little taller and slimmer.
Fate Worse than Death: Adam Monroe is stuck in a coffin underground, thanks to Hiro's teleportation ability. Did we mention that he is immortal? And that he essentially can't die? He suffocates, then regenerates, then suffocates again, etc...
He is released by Hiro in the next season in exchange for helping Hiro and Ando. Before he can do much of anything, he is kidnapped by an agent of Arthur Petrelli, who steals Adam's immortality/healing power with a touch, causing him to diefor good.
A Father to His Men: Danko. He admonishes Nathan for not caring enough about his agents, then later tells the rest of his team to remember two killed by a shapeshifter.
Subverted later when he's willing to sacrifice members of his team to allow Sylar to continue working with him undercover.
Also Danko's motivation in volume 5. Tracy is killing former members of his team, so Danko goes after her for revenge. Or maybe it's that whole Fantastic Racism thing again.
Faux Fluency: Since, despite apparently having a decent working knowledge of Japanese, Adam still pronounces Yaeko's name "Yay-ko", his Japanese is probably an example of this. And who knows how many other examples there are, since polyglots seem to grow on trees in the Heroes universe.
Fauxlosophic Narration: Mohinder's Book Ends mentioned above. Though in Volume Three, they mercifully switched to using actual poetry instead of MoeMoe's fluff for a time. They also let a few other characters have narration duty.
15 Minutes of Fame: After Claire rescues a man from a fire early on, she lets Jackie lie about being the one who did it (all anyone saw was that the rescuer was wearing a cheerleader uniform), since she herself is mortified about the existence of her superpowers.
Fight Unscene: Happens three times in "Five Years Gone": twice when Future!Hiro and Future!Peter square off against the cops and once when Future!Sylar and Future!Peter have their big showdown.
They pull the "seen only through a crack in the door" trick again in the Volume Four finale, when Nathan and Peter fight Sylar.
The penultimate episode ends with a villain with the power to multiply himself surrounding Peter and a now-good Sylar in Parkman's basement. The next episode begins with Matt, upstairs, being rescued by the pair, having already defeated the villain.
First Girl Wins: Charlie over Yaeko. Well, in the order that Hiro meets them. Hiro met Charlie in present-time in Season One and went back in time and met Yaeko in feudal Japan in Season Two. Except that Charlie also didn't end up being with Hiro in the end; she was trapped in the past and married a WWII soldier and then refused to let him change her life after she'd grown old.
First Episode Spoiler: HRG is Claire's father. Claire is also adopted and asks Sandra who her biological parents are, but we don't find out who they are until "Distractions".
Pretty much everybody, but Hiro Nakamura takes the cake - with his powers to travel through time / freeze time, there isn't in theory any villain he couldn't defeat or any situation he couldn't save. Hell, if you raise a whole army against him he can go back in time to the day before you started to raise an army, freeze time and kill you while you're taking a piss. So far there hasn't been a season finale climax / final confrontation which couldn't have been avoided had Hiro simply used his powers well had a brain.
volume 5, when Hiro goes back in time to save Charlie, does, by showboating his powers in front of Sylar. Then, Samuel kidnaps Charlie. Oh no, I better obey his wishes rather than go back in time to save Charlie, which I just did 5 minutes ago. To be fair, Hiro’s powers were malfunctioning but he still managed to travel back in time for Samuel in hopes it would help him rescue Charlie.
Even better, why not just have a future Hiro visit his present self, telling him where Charlie is. Then, after rescuing Charlie, present Hiro does the same thing. It's a stable time loop.
At the end of Season 3, Sylar kills Nathan. Angela and Noah decide to cover up the death by having Matt brainwash Sylar into thinking he's Nathan, despite the fact that Claire was elsewhere in the same building and they could have easily brought Nathan back with an infusion of Claire's blood, just as they did for Noah in Season 2.
Actually a plot point After Sylar meets bio-dad who attempts to steal Sylars healing powers to heal his cancer, gives Sylar a speech about all the things he is going to do when he is healed (pretty much all of them Evulz), which motivates Sylar (who was just pretending the whole to be caught).
Framed Clue: Chandra Suresh's diary is hidden inside the case of his laptop, and only discovered when Mohinder throws it down in frustration. There's also a very clumsy version of this involving reaching for some salt at a diner.
Franchise Killer: Season 4/Volume 5 ended up being the final season of Heroes, despite leaving a Cliff Hangar. Opinion is divided over whether or not it was due to Volume 5 itself, or just karma from arguably inferior previous seasons catching up. Actually, not only was the show cancelled, but they also ended up abruptly ending the graphic novels, and original plans for an end-of-series movie was also scrapped as well.
Sylar, made much worse because he has Joker Immunity to the power of ten.
Genocide Backfire: The whole cockup at the Coyote Sands Concentration Camp. Although not a deliberate attempt at genocide, it was a major effort by the U.S. Government to round up and contain supers; before you know it Dr. Suchong Dr. Suresh slaps a little girl, little girl blasts him with lightning, soldiers freak out and open fire on everybody, and hey nonny nonny you've got blood all over the place and a whole bunch of dead supers. And from the ashes rises two groups of very pissed off supers: The Company (who have been responsible for, among other things, attempting to nuke New York City and creating a virus capable of wiping out 99% of the Earth's population), and Samuel Sullivan (the super Anti Christ who, if powered by enough followers, potentially has the ability to split the Earth in half).
The Ghost: Mr. Linderman spent the first half of the first Volume as an invisible character. This was later revealed to be due to budget constraints. The show's budget wasn't big enough to pay for the high cost of actor Malcolm McDowell appearing from the start. In Volume Three, he appeared as sort of a literal ghost.
Good Thing You Can Heal: Claire Bennet is sort of the Trope Namer (it isn't a direct quote but might as well be due to all the trauma the writers like to put her through.) Lately, ever since he gained Regeneration, Sylar is giving Claire a run for her money, with getting shot, his shoulder dislocated, his throat slashed etc.
A God Am I: Adam Monroe, at least in the supplementary comic books. Also Baron Samedi, the Haitian's brother. He seems to give off major Xerxes and Colonel Kurt vibes, too. Let's not forget Arthur Petrelli, with his delusional Nietzche fixation.
Gravity Is a Harsh Mistress: There's actually a scene in the second episode where Peter is standing on a ledge talking to Nathan. Peter gets angry and starts walking towards his brother - off the ledge and onto thin air. He doesn't even realise he's doing it until Nathan points out the three feet of empty space beneath him, at which point Gravitational Cognisance apparently kicks in and he falls back to the ground. Justified in that Peter is unwittingly using his new flying ability, but the effect is still remarkably cartoony.
Have You Told Anyone Else?: When Noah Bennet asks this of Claire about her powers, she tells him that Zach knows and Lyle found out. The next day, Claire finds that their memories have been erased.
Have You Tried Not Being a Monster?: In Volume One, complete with Claire being asked if she plans to "come out" to her family. The Shanti virus (the original strain) also has some parallels to HIV.
Headphones Equal Isolation: Emma, a deaf character, wears iPod earbuds that aren't connected to anything to prevent people from trying to talk to her.
Heel-Face Turn: Mr. Bennet, whose various ruthless actions proved to be an elaborate stratagem to protect his daughter from the very company he's working for, and who is eventually outed and forced to join with two of the heroes in order to keep her safe. This seems more like a Reverse Mole, although the problem with both of these is that he still seems more like a Heel than a Face. Continuing to think of him as a Heel is seeming more reasonable all the time, as Claire (very) briefly flirted with going Heel in Volume Three.
Sylar starting in Volume Three. So many in fact that you think he'd get whiplash.
Finally resolved near the end of the series as Face.
Also Nathan Petrelli throughout the show. But then, he IS a politician...
Tracy Strauss: she's started as a political ally to Nathan Petrelli with a penchant for turning journalists into popsicles, who then jumps ship after being told she's a synthetic superpowered triplet and becomes Arthur Petrelli's office bitch, who then tries to "help" Peter and the others at the start of Volume 4 after Arthur kicks the bucket, who then breaks out of Building 26 captivity and is shot, whilst frozen, by Danko, who then returns as some killer ice queen/water-controlling wench with a serious grudge against anyone from Building 26, including Noah Bennet, who then goes a bit soft and gooey around Bennet when he offers her clam chowder after watching Danko get sliced to ribbons. Yeah, we got a little confused with her too.
She's related to Niki, who had a split personality. Only makes sense she's kind-of crazy, too.
Angela Petrelli could be an alternate title for the Trope.
Heroes: Obviously. Though it's somewhat subverted; the show seems to like exploring just how hard being a superhero would be like in practice.
Then subverted. D.L. takes a bullet from Linderman to save Niki. Enter season two, he is dead, and we are lead to assume that is how he died. But then a flashback to four months ago has him make a full recovery from the hospital, and is indeed well enough to go fight fires and stuff...only to get shot by some random crackhead with the hots for Niki.
Don't forget Niki Sanders, who tries to rescue Monica from a burning building at the end of Volume 2, without her super-strength. Monica gets out, Niki doesn't.
Daphne is shot trying to rescue Claire, Matt, and the others. She initially survived, but later dies from sepsis because Danko had her removed from the medical facility.
And Traci apparently sacrifices herself in a spectacularly permanent-looking fashion to prevent Danko from killing Micah/Rebel. The Volume 4 finale shows that she got better.
Nathan Petrelli flies off with his critically nuclear little brother Peter in the Volume 1 season finale. He also "gets better" after a sense in the next season... Then at the end of Volume 4 trying to atone for this Volume's douchery he goes up against Sylar by himself (ditching Peter in the middle of the battle) and gets himself killed.
Matt, after having his body possessed by Sylar, uses his ability to arouse everyone else's suspicions about him, leading the Texas police force to deploy a dozen men with guns to form a circle around him. In order to stop Sylar from going on a Roaring Rampage of Revenge against the people who stole his body, Matt makes the cops think Sylar has a gun, leading them to open fire, and effectively taking out both Sylar and Matt.
Eden, who kills herself to prevent Sylar from gaining her ability.
Peter also tries to pull one in "How to Stop an Exploding Man", but is saved at the last minute by Nathan.
Hidden Elf Village: This seems to be the purpose of Big Bad Samuel's Carnival in Volume 5. They're a bit more proactive than most, as Samuel's M.O. often involves secretly arranging the deaths of Muggles to push other supers into joining the Carnival.
Hitler's Time Travel Exemption Act: Mocked hilariously when Hiro repeatedly uses his power to sabotage a copier so that a goofball accountant won't photocopy his butt and get fired. Everytime Hiro stops him, he just does it again at the next party.
Honey Trap: Under Company orders, Elle is dispatched to get close to and encourage a pre-Sylar Gabriel to develop his burgeoning powers. She ends up falling for him, but it all goes heads up when he discovers she had been lying to him about not having powers. Needless to say, he was not happy to see her pop up in Mohinder's lab.
Daphne is also significantly shorter than her partner Knox (5'10") when they approach Hiro and Ando at the bar.
Sylar (6'2") and Elle (5'1").
Claire (5'1") and West (6'), Sylar...heck, any guy she stands next to (with the exception of Hiro).
Noah (6'2") and his subordinate Eden (5'3").
If You're So Evil, Eat This Kitten: Happens to Hiro at one point, when he is told to kill Ando. Hiro goes back a few minutes to get a trick sword and a bag of fake blood.
I Have You Now, My Pretty: Inspired by their Not So Different paths over the course of the series, Sylar woes a captive Claire in the Volume 4 season finale just before his attempt to become President of the United States. Especially creepy in that, by the series' timeline, Claire is barely 17 at this point.
Idiot Ball: It's like they're playing basketball with the damn thing. May even count as an aversion, in that everyone is so stupid all the time that it's out of the ordinary when one of the characters does anything intelligent. "Smart Ball", perhaps?
Beforehand, Hiro was persuaded by the carnival guy that he can change the timeline without doing too much damage. A few episodes later, the carnival guy tells Hiro that saving Charlie would screw up history...and he believed him despite that other encounter where the carnival guy says the opposite thing.
And how does Mohinder decide to fix his little problem? Well obviously by kidnapping people to experiment on.
Think of what Peter, Nathan, and Claire could have learned if they'd actually sat down and talked to each other at the end of ".07%"! Bonus points if they'd thought to bring Mohinder into the conversation, or, you know, their mom!
When Tracy Strauss is imprisoned by Nathan's men, one of her many powerful friends comes to inspect the building. Said friend is shocked to find Tracy in such conditions and promises to get her out. What does Tracy do afterwards? She breaks out of the prison and kills one of their men, turning her friend against her.
Idiot Hero: Peter, first and foremost, though he starts to grow out of it. Switches off between Hiro, Mohinder, and Nathan.
Claire, but other characters fall into this as well.
Parkman says this to Daphne in Volume Four. Claire, on the other hand, seems to have given up on any hope of a normal life.
Parkman, at the start of Volume 5, is trying to lead a normal life with his wife and son - trying to give up using his powers, attending drug rehabilitation sessions to try to keep his "addiction" under control. Of course, now he's got Sylar living in his head, this obviously won't last...
Believe it or not, Sylar.
I Just Want to Be Special: Seriously, don't mention being special around Sylar—it will only lead to tears and dissection. Also Hiro and Peter (at least until Peter learned the downsides of his ability), Monica too.
I'm Standing Right Here: In Volume 1 when Nathan gives a campaign speech on his "mentally disturbed" little brother. Naturally, Peter punches him right in the face afterwards in the parking garage as Nathan was getting ready to leave.
Important Haircut: The show lives off Hair Tropes like a king. Aside from the Evil Hair Gel mentioned above, the best example was Sylar (mercifully) cutting Peter's trademark Emo bangs.
Improbable Weapon User: Mohinder has attacked people with things like tuning forks, syringes, microscopes, rolling chalkboards, elephant sculptures, tables, fire extinguishers, and taxi doors with an astonishing rate of success. We're nearing "In the average living room, there are 1,242 objects Chuck Norris can use to kill you, including the room itself" territory here.
Informed Flaw: For all of Volume 3's talk about Sylar's uncontrollable "hunger", he seems perfectly capable of hanging around and interacting with other supers without eating fingerbanging their brains to see what makes them tick. This seems to be the case even after he turns back fully to the side of evil (he never chows down on Luke, for example, despite on multiple occasions being given a good reason to do so. Ditto for Doyle, who he must have been lugging around for more than a day). Peter Petrelli, on the other hand, pretty much chops open the head of every single person he meets after acquiring Sylar's ability, despite (unlike Sylar) receiving no apparent tangible benefit from doing so.
(Though in Sylar's case this could be because he spent Volume 3 working to get it under control for the sake of his (fake) family.)
This was an unforgivably poor explanation of Sylar's murderous impulses. If his power was responsible for him being evil, how do the writers explain his violent, power-lusting behavior during the second season, the entire duration of which he was powerless?
Addiction to power can be separate from addiction to knowledge.
What about in volume 5 with fake Nathan? Shouldn't he have felt urges? And also when Peter borrows fake Nathan's powers. Shouldn't Peter have been overcome by the urges again?
In Spite of a Nail: "I Am Become Death" shows Nathan as President and Peter as a scarred renegade — the same as in "Five Years Gone" despite other major differences. And as of Volume Four, "Five Years Gone" seems more likely than ever.
In the Blood: According to Momma Patrelli, it's not Sylar's fault he's a mass murdering psycho; his powers ("The Hunger") just drive him to murder. Oh, okay...
Not really a retcon, per se. it doesn't contradict anything previously shown and, in all fairness, it's been made pretty clear that even without his powers he's still a killer as he was perfectly willing to help Elle kill Noah and abduct Claire after "The Eclipse" stole his abilities. It's just that his powers give him a thirst for abilities.
Instant Sedation: In Volume Four, the Building 26 teams stick tubes up the noses of captured "specials" that release some sort of gas that instantly sedates them. The inverse is also the case: when the tubes are removed, the victims instantly wake up again.
Invincible Hero: Peter. The writers realized this in Season 2; unfortunately this lead to him getting Easy Amnesia in the first half of the season and carrying a massive Idiot Ball in the second instead of having it fixed in any meaningful way. Fortunately, they learned from their mistake and reduced his power significantly in Volume 3(He can now only copy one ability at a time).
Invulnerable Knuckles: Peter shakes his fist in pain after clocking Sylar in the mouth for making an insensitive comment about Emma. Oddly enough, this takes place inside Sylar's head, so the pain should have been at least imaginary.
And in their Kirby Plaza altercation, Peter's fists made contact with Sylar's face enough times for Sylar to spit up blood and Peter's radiation ability started to go haywire.