There is so much HoYay in this show that even after only one season had aired, a damn flowchart was needed to keep track of it all.
Note that this chart only describes Ho Yay from season one and that seasons 2-4 added plenty more Ho Yay (and also Les Yay) to the show.
Peter and Nathan Petrelli are much more touchy-feely than a pair of American brothers would usually be. That's all I'm saying...
First season, there's a scene where Nathan visits a comatose Peter in the hospital, and kisses him on the cheek before leaving. In the cast commentary for this scene, the actors themselves commented on the subtext.
And Mohinder and Sylar seem strangely close, even after Mohinder figures out who Sylar is.
Not just strangely close, but kinkily close. After discovering Sylar's identity, Mohinder straps him down to a chair, leans down to breathily whisper in his ear "It's going to hurt," and then jams a big needle into his spine from behind.
Mohinder makes Sylar scream his own name during that scene. So yeah.
You know what they say, "You can't spell Sylar and Mohinder without S&M."
And after all this, Mohinder is still the first person Sylar calls when he's frightened, even before he calls his own mother.
And that in the dystopian alternate future shown in the first season, Sylar disguises himself as President Nathan Petrelli, and keeps Mohinder by his side as his closest advisor for several years. At one point he chides Mohinder "You haven't slept in five years," prompting an explosion of fangirl speculation as to how exactly he knew that.
And that in their very first meeting, Mohinder remarks on Sylar's brown eyes, while Sylar compliments Mohinder's coat.
Hiro and Ando are the sort of partners who go everywhere together—literally, to a certain extent.
Mobster: You guys are going to the bathroom together? Ando: Yes. It is how we roll.
And Claude sure does like to beat Peter up with a large stick, which isn't symbolic at all.
Oh, and each shoved the other against a wall/pole at some point.
In the second season, Matt and Mohinder are raising a little girl together.
And know each other well enough to snark on each other's Daddy Issues when they have a spat.
And Kensei/Adam even says to Hiro, "You were more than a friend!" and "You taught me how to love."
In volume 5 when Hiro is put on trial (it's all in his head) for misusing his powers, he says it was "For family *looks towards Kaito* and friends *looks towards Ando* and love *looks towards Adam*."
Anyone else find it kind of odd that Adam was still calling Hiro by his pet name despite the fact Hiro just put him six feet under?
Speaking of Adam/Kensei and Ho Yay, why hasn't Adam and Peter been mentioned yet? Really, the fact that Peter absolutely refuses to believe that Adam is up to no good, despite several reputable sources telling him that Adam's bad news just adds to this. Peter only believes that Adam's a bad guy when Nathan tells him so. Sorry Adam, your apocalypse plan was ruined because Peter's Ho Yay with Nathan was stronger than his Ho Yay with you.
Matt and Nathan refuse to talk about how they got from New York to Texas. Suffice it to say that this is not a fandom that shies away from finding subtextanywhere.
The season 3 episode "Eris Quod Sum" throws Claire/Elle a few bones. The biggest one has to be when the two of them actually form a truce and travel to Pinehearst together by plane. Elle (who's suffering from lack of control over her powers) has a bit of a freak out and almost sends the plane spiraling downward with her electrical charges. Claire tells her to dump all the excess electricity into her since it won't harm her and she does so by holding her hand. Once the trouble passes, they breathe a sigh of relief, notice they're still holding each other's hands and immediately let go.
In the online commentary for one of the later episodes of the second season, Sendhil Ramamurthy comments that Mohinder and Peter look as if they are about to kiss after meeting for the first time in several years (this being the alternate future).
The online comic replaced the picture Isaac drew of Peter kissing Simone with Peter kissing Mohinder. Seriously.◊note (Admittedly, the artist was trying to draw Simone, but since he did not watch the show, he had drawn her with shorter hair and darker skin...accidentally making it Mohinder instead.)
In one of Peter and Mohinder's earliest scenes together, for no apparent reason there is a distractingly huge sign in the background that reads "DON'T GIVE YOUR HEART TO JUST ANYONE." I Am Not Making This Up.◊ Some fans have had a field day speculating about the subliminal message going on...
The case could also be made that it's a form of Ship Sinking, as in, "Peter and Mohinder should not give their hearts to just anyone, meaning each other." Still, it's a testament to the rampant HoYay on this show that literally only three episodes into the entire series, there was already a slash ship that needed to be sunk.
This Troper even recalls a certain commentary by the creators on the meeting of Nathan and Peter right before the end of the Season 2 season finale where the brothers were intended to kiss... "because they're Italian." The kiss was cut, but you can see an awkward pause right before they hug.
This troper just got some Ho Yay from Fridge Logic (or Fridge Brilliance, depending on preference). At the end of the graphic novel "The Ten Wives of Takezo Kensei", Adam says his "eleven bride" is going to come rescue him. But then it turns out to be Hiro who saves him in season 3. Is it the writers just ignoring the awesome online novels and their awesome plot hook, orrrrr...
This is actually the product of They Wasted a Perfectly Good Plot. Notice how he mentions one of the surnames he took on during those 400 years was "Sanders," and how Angela's dream showed Adam rescued by Niki Sanders' sister, Tracy.
The Peter and Sylar Ho Yay got more obvious with Peter going inside Sylar's mind and being trapped the dream world with him for years (hours in reality) complete with arguing in each other's faces and innuendo-laced conversations. You can imagine what they might have done to pass the time aside from hitting that brick wall. Once they break out of the dream-world, Sylar asks if it was real and Peter only offers a small smile. Eli then shows up to stop them from helping Emma and apologizes for breaking up "the love fest".
In the season finale "Brave New World",a shocked and very unamused Parkman confronts them on how they escaped Sylar's mental prison and they simply reply in unison, "It's a long story".
Peter even tugs Sylar by the arm as they leave for New York, and the two of them share a look when they arrive at Central Park. Sylar then gives Peter a reassuring pat on the chest at the carnival before they split up to find Samuel and Emma. Let's just say that "The Wall" and "Brave New World" were just rife with the Foe Yay-turned-Ho Yay for these two.
One fight between Peter and Sylar had their faces nearly touching in between punches. The same fight had Peter clutching Sylar◊ and flying him into a window grill.
They have another encounter in Sylar's prison cell and both just happened to be wearing only very thin pants and undershirts.
In "Building 26", we meet an Indian woman who runs a store with her best (female) friend, and tries (successfully) to get out of an arranged marriage. She even tells her grandfather that perhaps "a traditional marriage is not my destiny", while making significant eyes at her partner. Many of the fans have drawn the obvious conclusions from this.
Sylar has recently picked up a Sylar wannabe on his seasonal road trip, Luke, who hero worships him, tries to impress him (in a teenage boy kind of way), and keeps making sexy time eyes at him. Sylar is not totally annoyed by this- after ditching Luke to government agents in Building 26, he goes back to get the agents' gear and rescues Luke as an afterthought.
From the Volume 4 finale:
Bennet (to Danko): ...and then you got into bed with Sylar.
It doesn't help that Heroes can't seem to make marriages or relationships stick. Pretty much Everybody is Single, with divorce and/or death of the other partner being ridiculously commonplace. In V2, both Matt and Nathan's wives were Put On Buses. Matt moved into Mohinder's apartment and raised Molly with him, and Nathan became a drunk who moped about his (presumed dead) brother all the time. Sandra and Noah's marriage, the only one to have lasted through all three seasons, is currently on the rocks. No one is surprised.
Noah and Sandra have divorced. Matt has actually repaired his marriage, but we don't know how long that's going to last.
It's not going so well, due to... uh, do yourself a favor and just watch. The Dork Age is over.
And the Les Yay comes back with a vengeance with Claire and Gretchen in Season Four (Volume Five).
Turns out Gretchen is actually bisexual, and is crushing on Claire. Claire's feelings on the matter are uncertain, but she does value Gretchen as a friend. (Gretchen was pleased - uncertainty means there's a chance!)
As of last we saw, there was hand-holding, possibly as a couple for real. Initiated by Claire.
More Les Yay, this time between Claire and Tracy in "Brother's Keeper", when Tracy was going through panic attacks and she went to Noah's place for help, but found Claire instead. Claire helps Tracy settle into a warm bath when another panic attack happens. Claire tries to calm her down, but she freezes Claire instead, breaking Claire's foot. But she healed and there was no hard feelings about it and they used Claire's frozen severed foot (she grew a new one) as a centerpiece on the table. Mr. Bennet comes in later and finds them chatting together on the couch wearing nothing but bathrobes.
Samuel and Edgar anyone? Samuel is extremely touchy-feely around Edgar (and Lydia). Samuel's creepy pervert smile adds to the subtext.
Samuel has absolutely no sense of personal space around Edgar or Lydia. Samuel's behavior around those those is one of the reasons why some fans refer to him as the "boundary fail carny king". There's a reason why these icons exist.
In the third episode of the web series "Slow Burn", Samuel catches Edgar with money that he thinks he stole from other people at the carnival. Samuel goes on about how Edgar should be severely punished (in a breathy voice) and asks Lydia her opinion on how they should punish Edgar. The episode then ends and the viewer never finds out what they did to "punish" Edgar. So, we've got the kink factor, Ho Yay and potential threesome set up.
Samuel and Sylar have quite a bit of tension when Sylar appears at the carnival.
This is more of a general example, but every time two characters have a Super Serious Conversation (which is usually at least once or twice an episode) they have to have this conversation about four inches away from each other's faces and it often looks like they're about to kiss. Here's a Sylar/Peter example from "The Wall" ◊ If you just look through some Heroes screenshots you can find numerous other examples.