Derek and Scott have THE MOST homoerotic tension in the show. It's mainly on Derek's end however. He's obsessed with getting Scott to be a part of his pack and took it hard when it appeared Scott betrayed him. He spends more time with Scott over the past two seasons than anyone else on the show. Season 3 already hints they're going to spend more time together, but as an added bonus one interview with Jeff Davis himself says Derek will grow into a nicer and better person because of Scott.
Derek manages to get smolderingly broody and completely ignore the personal space of practically every other male in the show, though Stiles does deserve some special mention.
Jackson winds up getting into a dance-floor threesome with Erica and Isaac, who are trying to get close enough to tranquilize him with a syringe full of ketamine. Gets an added layer of creepy if you know that ketamine is popular as a date-rape drug.
Derek/Stiles. They end up saving each other's lives more often than not, Derek, as mentioned above, likes pushing Stiles against walls, and there's that thing where they were holding each other in a pool for two hours. "Sterek" Shipping has become extremely popular in the fandom, and is openly played with by the actors in a variety of fan videos and photo shots.
Said pool holding occurred in an episode where Stiles is repeating word-for-word Allison's love notes to Scott and Jackson wants Danny to watch a video of him in bed and says he's EVERYONE'S type.
The Derek/Stiles subtext is almost text by now, to the point where a character openly states that he thinks the two make a good pair after a paralyzed Stiles falls on top of the already paralyzed Derek.
The writers certainly seem to be playing along with this in Season 3 which contains two fairly suggestive fisting references (particularly where Stiles pulls on a long latex glove whilst Derek is bent over a table), a scene where Stiles is slapping Derek awake whilst straddling him (combined with some very odd camera work...) and a LOT of intense eye-locking.
It's actually kind of funny if you think about it. In the first season, whenever Scott and Alison were on a date (which was a lot), Stiles and Derek were together. Basically, they were being written with the same function as the Beta Couple trope but without the kissing.
Stiles and Scott have this in spades, what with being each other's Heterosexual Life-Partners. They have no problems flirting with each other at all, and Stiles actually offers to make out with Scott. And then they say things like, "You have me, life fulfilled" and "Yeah, but I always had you". And have said I love you to each other. And spend so much time together that Stiles gets a key made for the McCall house and their teachers joke about them having separation anxiety when they're separated in class. Hell, in the first ten minutes of the show alone, Stiles sneaking into Scott's house is a common enough occurrence that he doesn't see anything wrong with it, and Sheriff Stilinski automatically assumes that wherever Stiles is, Scott must be too.
Knocked up several notches by "Motel California". Scott's driven to suicide by a combination of his guilt over screwing up people's lives, his grief over Derek's "death" and being under the influence of wolfsbane. Stiles talks him down before stepping into the puddle of gasoline and gripping the lit flare Scott's planning on using to kill himself. Definitely very Romeo and Juliet-ish.
Stiles: Scott, you're my best friend and I need you. You're my brother. If you want to do this, you're just gonna have to take me with you.
That entire scene with Stiles stepping into the gasoline with Scott showed that Stiles was willing to die along with Scott. Stiles even told Scott that if he (Scott) killed himself, "he would have to take him (Stiles) with him (Scott)". This scene was a testament to how much Stiles loves Scott and how he is willing to die for him and die with him. Totally something out of a romance storyline. Not even the best-est of friends and romantic couples have the degree of love and devotion that Scott and Stiles have for each other.
In "Lunar Ellipse", during Scott's monologue at the end, Scott says he looks for his friends, and the camera pans over the official couples (Danny and Ethan, Lydia and Aiden) as well as those who have the subtext there (Isaac and Allison), and then the camera cuts back to Scott just in time to see Stiles show up and grab onto him and Scott's face positively lights up in happiness. Yeah.
The end of "The Overlooked" has Scott agreeing to join with Deucalion to take down Jennifer, and Stiles pleading with him to not go, that they can figure something else out, with tears in his eyes, and Scott's equally heartbroken when he says "not this time". If you analyze the scene and take out the actual context, it almost looks like Scott is breaking up with Stiles and Stiles is begging his boyfriend not to leave him.
Dylan O'Brien, who plays Stiles, even referred to Stiles as being Scott's girlfriend, and had compared Stiles to being the girlfriend of a superhero.
There are many people who think that Teen Wolf is the love story of Scott and Stiles. Not even Scallison and Stydia could compare.
Jeff Davis, the creator of the show, has openly stated: "I've always said that the real romance on the show is with Scott and Stiles".
It should be noted that other than his father, the only other person that Stiles has repeatedly gotten overly emotional about or cried over is Scott. Most of the times when Stiles has cried on the show, it has concerned or been about either his father (especially if he is in trouble) or at the very thought of losing Scott or Scott being hurt or harmed under any circumstances.
Let's not forget Stiles' obvious irritation towards Isaac in season three. One could assume that Stiles acts catty or snarky towards Isaac because Stiles is jealous of Scott and Isaac's close bond and relationship. Isaac is moving in on Stiles' man and Stiles does not like it one bit! All of Stiles' catty and sarcastic reactions, comments, and remarks towards Isaac make Stiles come off as an ex-boyfriend scorned or Scott's jealous ex-boyfriend who Scott had broken up with for Isaac.
This seems to be a Running Gag in the series with Stiles showing jealousy towards anyone who gets close to Scott or develops some sort of a relationship with him. In season 1, Stiles seemed to show some minor and subtle jealousy towards Scott growing close with Allison and developing a romantic relationship with her. Stiles probably started to feel this way because Allison "replacing" Stiles in many ways and Allison was quickly becoming the most important person in Scott's life. Throughout season's 1 and 2, Stiles also didn't like Scott hanging around Derek either. Stiles has even suggested or complained to Scott to stop being overly concerned or worried about Derek. This same pattern extended to season 3, with Stiles showing jealousy and obvious irritation towards Isaac and Scott developing a bond with him.
In 3.18, when Scott is in the hospital room with Stiles while he is being examined, Stiles tells Scott that he has the same condition or illness (called frontotemporal dementia) that his mother had before she died. Stiles says there is no cure. Scott tells Stiles that if there is no cure, then they'll do something. He'll (Scott) do something (implying that he would give Stiles the bite). Cue a long loving stare from Stiles to Scott. And then a very tender and long hug between Scott and Stiles, where Stiles is basically clutching to Scott and even closes his eyes and rests his chin on Scott's shoulder. Oh, the feels.
Taken up several notches in 3.19 in the ending scene between Scott and nogitsune!Stiles. Stiles stabs Scott in the stomach with a sword (swords are known to be a highly phallic symbol), is incredibly touchy feely with Scott (face stroking and all) and as Stiles is absorbing the pain out of Scott, Stiles looks like he's having a major orgasm while he's touching Scott. Not to mention that Scott and Stiles are also soaking wet. Overall, the scene is highly sensual and homoerotic in nature and is probably the most homoerotic scene between two male characters in Teen Wolf history.
In the beginning scene of 3.20, when Scott finds out that Stiles is checking himself into a mental hospital, Scott looks so heartbroken when he finds out that Stiles is locking himself up for 72 hours. Scott's reaction to it was like he had found out or discovered that the love of his life was moving across the country or across the world. Scott tells Stiles that by locking himself up in a mental hospital, he can't help him. Stiles then gives Scott an affectionate look of both love and concern, saying "And I can't hurt you." Scott tells Stiles that he is willing to do anything, find anything and do everything to help him. Stiles then proceeds to walk up to Scott's face to the point where it looks like Stiles was going to kiss Scott. After telling Scott to make sure that he doesn't get out of the hospital, Stiles proceeds to give Scott another tender longing look. As Stiles walks away, Stiles looks back at a heartbroken and worried Scott one last time. Oh so much boy love between these two. These two should just cuddle and kiss already.
The fact that Stiles was willing to lock himself up in a mental institution through the major motivation of not hurting Scott again, shows just how much Stiles loves and values Scott and is trying to protect him as much as possible from himself (Stiles).
In 3.22, Allison tells everyone that nogistine!Stiles feeds off of strife, chaos and pain and that it is what he wants, for everyone to get overly emotional, stressed and chaotic. Nogitsune!Stiles then tells Allison and everyone else in the room that it's not exactly what he wants and that he was hoping to see Scott was around instead. In the text, it sounds as though the nogitsune is speaking about Stiles' innermost thoughts, desires as well as speaking from Stiles' subconscious. The fact that nogitsune!Stiles admitted to wanting Scott would imply that the real Stiles wants Scott deep down.
Let's not forget that Stiles ended up defeating the nogitsune after listening to Scott's Alpha howl. This implies that Stiles' love for Scott was what got Stiles to fight the nogitsune and fight for his life and come out of possession. This is The Power of Love and The Power of Friendship all rolled into one at work between Scott and Stiles, ladies and gentlemen.
After Stiles gets out of possession by the nogitsune via the nogitsune (which turns out to be a evil, dark clone of Stiles himself) vomiting him (the real Stiles) up, Scott is immediately able to tell which one is the real Stiles and which one is dark!Stiles. As Scott is unwrapping the bandage off of real Stiles face, Scott tenderly strokes Stiles' forehead and even brushes his hands over Stiles' chest. Also, the look on Scott's face is one of extreme concern and worry and relief, an expression that shows he is very glad that his best friend is back. The look that Stiles gives Scott in return is one of love, tenderness and confusion. Let's not forget that the first person Stiles looks at and sees after coming out of possession is someone that Stiles loves the most (Scott).
Season 3 already is a goldmine for the Scisaac ship. The first episode we have Scott being Isaac's second choice of emergency contact call. The second episode we have Isaac implying that he trusts Scott more than Derek and a lot of contact while Isaac is shirtless. The third episode has Isaac shouting concerned for Scott but not Derek. 3.04 takes the cake though. Isaac is able to get his werewolf rage under control when Scott shouts his name and later shows up at Scott's house in a soaking wet t-shirt asking for a "favor" (a place to stay since Derek kicked him out).
In 3.05 Scott almost dying prompts Isaac to attack and beat up an alpha (while in human form). While several people attempt to stop him, Scott screaming his name is what finally calms him down. In flashback it was also shown that Isaac absolutely refused to let Scott go off (presumably into danger) by himself, even though Scott was supposed to meet Deucalion alone.
The phrase "I love Mexican" could be interpreted as a Double Entendre when spoken to Scott...
Although her main love interest appeared to be Ennis, Kali had some very... suggestive vibes with Ms. Morrell and Cora. The LesYay went through the roof once Jennifer Blake appeared on the scene, with the revelation that Jennifer Blake used to be Julia, Kali's emissary, and Kali spared Julia's life after killing the rest of her pack. Sadly, it didn't end well.
In the "happy ending" scene at the end of the mid-season 3 finale, all the shots focus on couples: Lydia/Aiden, Ethan/Danny, Allison/Isaac and finally...Scott/Stiles.
Also of note, in his voiceover, Scott says that "Stiles and I both feel it. every day. Just like you said we would." in speaking of the feeling of darkness leftover after their shared near-death experience. Interestingly, Allison also went through the ritual with them, but Scott does not mention her, suggesting that he either does not know what she is feeling (because they are no longer as close as they once were) or he doesn't think about what she may be feeling, just himself and Stiles.
Allison and Lydia have plenty homoerotic tension, especially with Lydia trying to help Allison after the end of Season 3 Part A.
Allison and Erica during season 2 have a few Foe Yay moments, such as Erica digging her claws into Allison's thigh during class.
The season three episode "Galvanize" gives us Stiles explaining to Scott that, since he's an alpha now, he's basically the hot girl that everybody wants to be with. Stiles leaves just before Isaac arrives to see Scott thinking about it.
Isaac: What? Scott (completely serious): I'm the hot girl. Isaac (also serious): Yes you are.
Chris Argent/Derek Hale. What once might have been Foe Yay seems to have taken a turn into something more as Season 3 Episode 19. This episode begins with claws vs. guns, but they both put those away to work together, the Hunter actually warning the wolf to be "careful". They are arrested, and handcuffed. They banter at the station. Derek complains about being stuck, letting Chris know he could get out of the handcuffs but he doesn't, because Chris asked him not to. Derek insists he wouldn't risk his life to protect Chris is anything happened, but minutes later he uses his own body as a Human Shield to protect Chris from a bomb explosion.