Gauron has a lot of one-sided Ho Yay and Foe Yay towards Sousuke. Sweet mother of Freud, the guy constantly makes incredibly gay innuendos towards Sousuke, and implies that fate is what brings them together. Gauron apparently became Sousuke's Stalker with a Crush and fell in love with his "beautiful" cold and unfeeling eyes when Sousuke was twelve. Seriously-when Gauron first saw him, he literally did a double take, parked his jeep, and tried to pick him up. He keeps calling Sousuke "Honey," much to Sousuke's disgust. And then there's their fight during the finale of the first season, where Gauron hugs Sousuke'sHumongous Mechawith his own and pins him onto the floor in averyawkward position. Sousuke struggles to get away, and Gauron gleefully says things like, "let's be friends" and "I'm so happy, you've stuck with me till the end." Sousuke is shown sweating and panting, and Gauron's broken down mecha starts leaking thick white liquid onto his face with his trademark permanent Slasher Smile on it. Of course, Gauron's ultimate intention is to detonate his mecha with 300 kilograms of explosives and kill both of them (which might very well be his idea of getting to fourth base with Sousuke), but it looks for all the world like giant robot sexual assault. The manga even has him yelling out happily, "Yeah, that's what I'm talking about! Ah, what a rush!" And as impossible as this sounds, Gauron's moaning and loud orgasms are actually more pronounced in the novels, where he literally yells out happily, "RIGHT, RIGHT, RIGHT! FASTER! MORE! MORE!!" It makes Sousuke very unnerved and disgusted, and is pretty much what pushed Sousuke to conclude that this makes Gauron completely insane (as opposed to before, where he simply thought Gauron was excessively cruel). All in all, it's heavily implied that Gauron was genuinely in love with Sousuke in his own twisted way.
In episode 24 while Gauron's trying to blow himself and Sousuke up (possibly in his screwed-up mind, as a lover's double suicide), he cries out, "I LOVE YOU, KASHIM!"
About Gauron's line "I love you, Kashim!" — in Japanese, Gauron actually says "Aishiteru ze", which literally means "I love you" with all the romantic and sexual connotations attached to it.
And then, in the third season at their last meeting, he is shown acting like Sousuke cheated on him or something, being extremely bitter and jealous towards Kaname, calling her the "cancer" that changed Sousuke. What takes the cake, though, is that in the novels, Gauron actually tells Sousuke that he fantasized about killing Sousuke, dragging his corpse out of the AS, and then fucking it. And he says he always thought Sousuke had beautiful eyes... "like a saint of war" and an adorable face. Kinda romantic, really...
Gauron seems to have lost some of his edge and become even more messed up since falling for Sousuke... after all, if he didn't care about Sousuke, he wouldn't have been so very angry in the first place...
Which isn't helped by how Shoji Gatoh himself mercilessly teases at the idea of Gauron and Sousuke together. Humorously lampshaded in Episode 12 of Lucky Star (of which he was the writer of the episode) Sousuke is shown.
On the subject of Gauron's Stalker with a Crush actions towards Sousuke it's made especially obvious in TSR, where he orders the destruction of a huge city to lure Sousuke there, spreads an incredibly complicated and cryptic message that no one in the world except Sousuke would ever understand, orders the two beautiful girls who adore him to go to their deaths just so that he can Murder the Hypotenuse all for the sake of his obsessive and sick love for Sousuke. He also apparently knows a lot of information about Sousuke's background and history that he shouldn't even know (considering that no one else in the series, including Kalinin, knows some of that stuff), making it very likely that he researched and stalked Sousuke even more than what was shown. Something worth noting is that, as shown in the novels, he was actually recording and watching footage of Sousuke without Sousuke even knowing. Gauron's partner is shown to be disgusted and annoyed by Gauron's euphoria and ecstasy at watching "his precious boy." And when Sousuke goes alone and finds out that Gauron is still alive, he expects Gauron to get his two underlings to kill him (or at least ambush him and do something of that sort). Instead, Gauron is shown to be genuinely delighted to see him, and offers Sousuke something to drink (though it has to be "self service," since... well, he has no arms or legs). Sousuke is shown to be in disbelief about the general friendliness coming from him, and tells him to "get real" when Gauron tells him he missed him.
He pretty much lost all of his limbs from sharks eating them, lost an eye, and half of the skin on his face (on the same side as his lost eye) had become keloidal. Of course, the guy ends up being able to hold on like that for six months, and it's implied that the only thing that sustained him was his desire to see Sousuke again. He's shown to be insanely happy to see Sousuke again, and although most of his last words to Sousuke only seem to piss Sousuke off, he does end up giving Sousuke an important clue ("Badham") that was necessary for a future mission. The rest of his last words were mostly for his own self satisfaction, screwing with Sousuke's mind because he's crazy that way.
Gauron's one-sided Ho Yay is pretty much completely canon. Watch the TSR comedy radio show where Gauron acts as the school's "sensei." Gato is doing this on purpose. Gauron orders Sousuke to write on the chalk board "Kashim loves Gauron Sensei. Heart. ♥" as well as "Gauron Sensei's extreme attack makes Kashim's heart pound. I want to have children with him." Followed by what appears to be an attempt to rape Sousuke in front of the class. Yay for subtlety.
There's also him joking that he has a picture of Sousuke naked and playing in the water.
There's fanart depicting Gauron showing off said picture...
And speaking of Gauron, he seems to have lost some of his edge and become even more messed up since falling for Sousuke... after all, if he didn't care about Sousuke, he wouldn't have been so very angry in the first place...
This is actually brought up and symbolically implied in the novels (though apparently parts of it were lost in the fan translation). Members of Amalgam actually covertly bring up to Sousuke how Gauron was overtaken by "cancer," all while mentioning that he "really really liked Sousuke"... and according to the original wording, a parallel is implied of Kaname being Sousuke's "Gan" (cancer), and Sousuke being Gauron's "Gan". Of course, any possible double meaning was lost to Sousuke. In addition, reading about the overall attitude of Gauron's colleagues when they talk to Sousuke, it seems like it's a well known fact to them that Gauron was way too obsessed with Sousuke.
And then there's Zaied's attachment to Sousuke. Pretty much in the entire, short amount of time he was shown, he was constantly thinking about Gaussian Girl-like memories of Sousuke, and whispering his name. He has fond memories of playing naked in the water with Sousuke, and he is shown to have been watching Sousuke while he was sleeping. The implications of that are made a bit clearer when one considers the novels, where Sousuke notes that he always had the odd feeling that the fellow guerillas he worked with treated him especially nice, and seemed like they were ready to jump and rape him when he was asleep just because he was so darn pretty. And although Sousuke doesn't hesitate to kill him, at the end, although he had his gun pointed at Sousuke and could've killed Sousuke with his last energy, he chose not to, and instead fired his remaining ammo into the air.
Some Lampshaded and teased Ho Yay / Foe Yay is found between Tsubaki and Sousuke, with their constant bickering. In the last episode of Full Metal Panic? Fumoffu, when Tsubaki thinks he's going to die, he even tells Sousuke that confessing to the girl he loves isn't as important to him as having one last fight between them. Matters aren't helped when, in one side story of the novels, Tsubaki makes a mistake and accidentally confesses that the one he loves is Sousuke. Afterwards, Kaname is shown to giggle and discuss who would be the submissive "receiver". She says both of them are.
In the Sigma manga, there's also the backstory between Sousuke and Kalinin that... can have a lot of Ho Yay subtext. Unfortunately, Kalinin is way older than Sousuke, and is supposed to be his legally adopted father. Just the whole way that Kalinin keeps going on and on about how Sousuke and him were "destined" to meet and be together, and how he gushes on about how they're inseparable. And then there's how guilty Kalinin felt towards Sousuke's beautiful mother... only for him to meet Sousuke again and see Sousuke be the spitting image of his mother. He then becomes obsessed with becoming a "happy family" with Sousuke.
Melissa Mao appears to have some attraction Bi the Way towards Tessa.
For example, on at least one occasion, Mao got completely drunk and decided to climb into Tessa's bed. Or the completely out-of-the-blue decision to grope Tessa's breasts underneath her shirt after Tessa passed out from getting drunk. Or the Hot Springs Episode from Full Metal Panic? Fumoffu where Mao starts rubbing ointment on Tessa's naked butt and then Mao starts moving on to other places and Tessa is heard telling Mao not to "stare at me like that!''
And in the Full Metal Panic! novels, Lemon seems to be Bi the Way towards Sousuke. Sure, he has a crush on Nami... but she also did a whole lot more to warrant it (stripping jokingly in front of him, offering to prostitute herself for money from him jokingly, holding his arm while her breasts press against him, and putting him in a situation where he accidentally found himself groping her breast). And then there are the numerous times he's shown to have a strong attraction to Sousuke, despite Sousuke not even doing much besides being good looking and simply being there. When he first saw Sousuke, he thinks to himself that Sousuke is verygood looking and "charming," despite Sousuke being completely emotionless (read: "eye candy"). Later, after Sousuke wins a tournament that helped win back Lemon's money, Lemon hugged Sousuke with "more passion than a french kiss would warrant," making Sousuke slightly uncomfortable. And later still, Lemon gets drunk, and subsequently invades Sousuke's personal space by hugging and groping him while blushing - which irritates Sousuke to no end.
Yu Fan and Yu Lan. You know those two twin sisters who Gauron adopted? Oh boy...Taking very intimate showers together...holding each other at every available opportunity, hugging their naked bodies to each other while kissing each other on the lips...Also Yu Lan sees Yu Fan descending naked from the sky toward her when she dies. Not to mention they intertwine fingers after one of them receives a pistol whipping from Gates.
Plus, in the novels Yu Fan and Yu Lan are actually male instead of female.
In episode 11 from Full Metal Panic? Fumoffu, a Camp Gay male trio from the Music Club challenges Sousuke to a bet — if he can pick up a girl, they'll pay for his meals, but if he can't, he has to... swim in a lake, naked, while they watch. It should be noted that when the Music Club announced this bet, numerous male students actually happily yelled out, "All right, Music Club!" He loses the bet (due to acting overly scary and violent), and they are way too eager to see him naked, chanting for him to "strip!" (and they're even shown leering, smiling, and blushing).
And then in the manga there's a substitute swim teacher who takes an immediate interest in Sousuke and his abilities — an interest which apparently involves blushing, drooling, and having thoughts which are WAY too suggestive to not be taken as Hot for Student. And he is shown to be very obviously jealous and shocked when he interprets Kaname's "I work well with Sousuke because we have a bond" as being that they've done it.
Another Ho Yay (albeit VERY No Yay) example: In an episode from Full Metal Panic? Fumoffu an elderly janitor from Sousuke's school is shown having a fantasy of having a threesome with Sousuke and Tsubaki. In his creepy envisioning of what he thinks is about to happen, chains are abundant and roses are used as censors. Yuck.
When Sousuke was a child he elicited the I'm Taking Her Home with Me! kind of response. His Cuteness Proximity was so incredibly intense, it managed to melt the hearts of war-hardened veterans and pretty much made them internally Squee that they want to take him home and make him their child. Which they then proceed to attempt to do. He certainly never lacked people who were all too eager to take him in as their own. Starting with Majid, an Afghanistani Helmajistani rebellion leader whom Sousuke had tried to assassinate, who liked him so much that he adopted him as his "Son of Bdakshon's Tiger," and raised him with complete kindness. And then there was Kalinin, who wanted Sousuke as his son from the very beginning, and took Sousuke as a prisoner of war after Sousuke tried to assassinate him. He then proceeds to persistently try to get Sousuke to agree to be his adopted son (which Sousuke refused, since he already had Majid as his "father" - yes, it got to the point of being a first-come-first-serve basis). After Majid dies, Kalinin finally manages to force his way and get Sousuke to be his legally adopted son. And all while that was going on, Gauron had tried to take Sousuke for himself ever since the moment he first set eyes on the boy. He literally did a double take, parked his jeep, and tried to lure Sousuke to come with him by promising him food and ammunition. Sousuke refuses, and Gauron ends up being unable to forget him for the next five years. (Though in Gauron's case, it's more of a pedophile rapist, sexual version of wanting to take him home, unlike the previous two).
Kurz and Sousuke. Kurz actually appears to flirt with Sousuke at times. And all their bickering comes off making them sound Like an Old Married Couple. And then there's those scenes in season 1 where we see a shirtless Sousuke being bandaged by Kurz.
Kyoko and Kaname. They're best friends and get along well. Also, when Kyoko meets Kaname when Kaname's at the hospital, they almost died, and you think some intimacy would be in order, but a Marshmallow Hell? And motor boating? Whatever floats Kyoko's boat.