In the Japanese version, Zelos calls Lloyd "hunny," a term he otherwise reserves for females. In the English version, it's changed to "bud" except in two obscure scenes the censorship squad apparently missed. (Yes, his butler also calls Lloyd Sir Hunny.) There was also a world map skit that was apparently too gay for America.
Also, one skit in which they missed the "hunny" might not have been such a mistake after all. It's called "Combo! Lloyd and Zelos," and it only occurs if Zelos is your top-rated character by Relationship Values. Perhaps that was intentional...?
You could also say Zelos is hiding behind a Have I Mentioned I Am Heterosexual Today? facade and Lloyd never shows much interest towards the female sex in THAT way... due to being a Chaste Hero or something else? The game has pretty much given you everything you need to ship it.
One good example of a specific scene is when the party is in the sewers trying to sneak their way back into Meltokyo. Just as they're almost through, Regal makes his entrance by taking Zelos hostage. Presea chases Regal off of him and the first thing he does once he's up is to go to hide behind Lloyd, latching onto him from behind. That's not the last time he glomps Lloyd either.
It's even more blatant and serious if you make Zelos Lloyd's most important person and get the bonding scenes with him - of course, you get romantic subtext with anyone you decide to pair up with Lloyd, but in Zelos' case Lloyd becomes basically the only reason he bothers keeping alive.
Well not exactly, Zelos only commits Suicide By Cop in the path where you re-recruit Kratos, since that's the only path where Lloyd doesn't insist that he still trusts Zelos even after he betrays the party. So this basically holds true even when he's not Lloyd's most important person.
Zelos is also the only person, besides Colette and Kratos, but he's a different kind of special case, who will give Lloyd a trinket of some kind after their scene in Flanoir - the trinket that will later save Lloyd's life from a trap. That makes two optional scenes in which Zelos is explicitly set up in parallel with the official love interest, to say nothing of the fact that he's actively Colette's mirror through the rest of the game.
Also with Zelos's relationship values maxed out, when entering the coliseum as Lloyd, Zelos will demand you "put on a show that will make me fall in love."
To which Lloyd responds not with Squick or snark, but with "Okay!"
And more between Kratos and Yuan, the latter of whom winds up cradling the former in his arms at one point.
This troper saw more Yuan and Botta.. So, so much Ho Yay.
Can't forget Mithos and Genis, either - they even get a sidequest together for bonding.
And in the sequel, after Emil learns that Regal was forced to kill someone he loved, there's a skit where Emil wonders if he'd be able to fight Richter if the time came. Followed by the fact that he doesn't like Richter "like that". In his own internal monologue.
The way Emil babbles on about how much he admires Richter despite the latter declaring himself to be Emil's enemy sure makes it sound like somebody has a man-crush. Not to mention, they're practically pitch-perfect for the seme and uke roles.
Emil also has slightly less blatant but still noticeable moments with Regal and Lloyd. Also he thinks Zelos worships Lloyd, and if you get Genis' conversation with Lloyd in Flanoir you'll see he still hasn't got over Mithos.
On top of Emil's obvious man-crush on Richter, even Richter and Aster have prime shipping opportunities as well. Man, Namco. So much Ho Yay, so little time. They certainly know how to please the fans.
In Flanoir where you first meet Decus, with his whole "You must have a crush on me too!" thing. He basically called dibs on Emil if things didn't work out with Alice...
Some people have started shipping Kratos and Lloyd only to find out Kratos is Lloyd's daddy.
Tales of Vesperia: If, after some twenty hours at least, you haven't done some serious thinking about how much Rita is concerned about Estelle's well-being, then, friend, you're not paying any attention. Makes one wonder just what it is she finds in Rita's drawer not long after they meet.
The PS3 version even adds some newscenes where Rita and Estelle pledge their eternal friendship and raise a baby together.
As soon as you enter the first dungeon with Rita, she is caught by the main character, staring at Estelle with little blush marks. She doesn't continue to stare, but will get very flustered when the other characters tease her for being close to Estelle.
Adding to the Les Yay, Judith frequently tells the other girls "you look cute when you're X." To say nothing of Yuri and Flynn's could-be-interpreted-either-way friendship since childhood.
Actually, let's say something about that. It would really not be going far to say that Yuri's kind of obsessed with Flynn. The second line out of his mouth in the game is about Flynn. Before you find him in Capua Nor, Yuri will bring him up out of nowhere, like after curing Halure's tree, or when everyone sees the ocean from Ehmead Hill. He really does give off the impression that Flynn is all he thinks about, and that's before he offers his life for Flynn's during the sequence with Barbos trying to start a war in Dahngrest. And on Flynn's side, well, there's the Taking the Bullet moment in Zaude, the fact that he scoured the entire ocean to search for Yuri after his supposed death, and his constant worry that Yuri's not getting the credit he deserves for his heroic acts. Their admittedly tense relationship culminates in their Duel Boss fight - preceded by the line "everything I feel is in this sword," no less - after which they lie side-by-side in the grass for a while. Add to this dozens of extra scenes, sidequests and subtext moments and they start to rival Ristelle.
And just like Rita and Estelle, this is not lost on the characters in the game itself. Sodia is fully aware that Yuri is her main competition for Flynn's affections, which puts her attempt to kill Yuri on top of Zaude in a whole new light.
Also worth pointing out is Yuri's explanation for why he doesn't turn Sodia in for her crimes. He seems more angry that she's abandoned Flynn than about the whole attempted murder thing. Then he says he agrees with her about something, which turns out to be...well...this:
Yuri: I'm a criminal. I could be killed any time. Flynn is the perfect knight. A perfect leader. He doesn't need a criminal by his side.
One can't forget Duke and Elucifer. The latter's murder leaves Duke so bitter, he's prepared to sacrifice all of humanity as a means of saving the planet.
Not necessarily. We've seen that at least one of them can take on human form.
Tales Of Legendia has, on the Ho Yay side, Jay and Moses, who eventually become quite close - Jay (who's generally emotionally distant) even hugs Moses in the end. It also has quite a bit of Les Yay, especially between Grune and Norma; Norma seems to quite enjoy cuddling up against Grune's chest, though she might have been doing that to taunt everyone. Grune, for her part, seems bisexual given that she seems fine doing, that, with anybody.
Shirley and Fenimore. Fenimore's death is even the thing that pushes Shirley into a world-destroying rage.
And then there's Elsa. At one point, you encounter her walking around town with Chloe, and she insists they're on a date, to Chloe's embarrassment. In a later scene, Elsa falls asleep on Chloe's lap and repeatedly says her name in her sleep, then, upon waking, proclaims Chloe to be "the best".
Norma: It's love! True love!
Pick two characters in Legendia. Any two. Oh look, you have found a couple with a lot of subtext!
He's not just being sarcastic. Take, for example, the scenes Shirley and Chloe get together following the latter's day in the limelight episode (especially once Norma gets in on the fun, claiming Chloe is "hogging Shirl". The girl even has a segment where she starts fawning over Grune's breast size.) And of course:
Moses: All us baby, it's all us!" *faintly homoerotic hand clasp*
Guy is terrified of women, and acknowledged in one sidequest to have basically raised Luke as they were growing up together. As a result, Luke depends on him emotionally to a great degree. Add to that the fact that Guy is Luke's servant and therefore technically has to follow his orders.
Luke and Asch have a great deal of aggressive tension between them, plus Luke's struggle to have Asch acknowledge his right to exist, and Asch's Tsundere way of looking after him.
Some people are a little put off by the implications of Screw Yourself, because of the whole replica thing. Others say that just makes it hotter.
Dist is openly obsessed with Jade, only avoids Camp Gay because his sexuality never actually comes up, and generally acts like a Stalker with a Crush. Meanwhile, Jade tries to ignore him, but they were childhood friends, and the party actually speculates that Jade likes Dist more than he lets on. The interrogation scene with Jade and Dist was particularly...questionable. Dist also hates Peony and basically treats him like a rival love interest, which leads to the next point...
Peony refers to Jade as "his", and gives him privileges well above his rank and station purely because they're so close, and since he's the Emperor he can do that sort of thing. While Jade trolls everyone in the game, Peony is the only one who can get Jade back just as well, or even better. Jade is The Stoic, so he doesn't show as much affection as Peony does, but he does undertake dangerous missions as Peony's most trusted adviser, which speaks volumes. And then there's a scene in Tales of Fandom 2 where it looks like Peony has been assassinated, and Jade actually shouts his name. His realname.
Jade and Guy also have a bit of a bromance going, at the very least. In one skit when the party complains about how tired, sweaty and gross they are, Guy notices that Jade actually smells really good and compliments his cologne. Jade's got at least a little respect for him, as shown when he tracks Guy down at the Aramis Spring to ask for his help, even after the party has semi-disbanded, thanks to Luke. On a more heartwarming note, when Guy remembers what happened to his sister, it's Jade who's standing with him in the chapel. Oh, and then, of course, there's the skit in which Guy is tickle-tortured, which ends with Jade nibbling on him.
Tales of Graces.....oh boy. Richard's crush on Asbel seems to have started when they were kids, 7 years ago. And not to mention that in the demo for Tales of Graces F, when Asbel jumps for the ship it's Richard that catches him. First scene. Then there's Pascal and Sophie, and Hubert who seems to be some sort of backwards tsundere for his brother. And then Lambda. Lambda is....well, let's just say he spends most of his time residing in either Richard or Asbel and has yandere tendencies.
Not to mention, him giving Richard some yandere-ness as well. Just listen to the voice clips of him screaming Asbel's name like a betrayed lover.
What about the Future arc ending, and how Cheria and Sophie were practically dancing with each other?
The Future arc takes all the Ho Yay to eleven. Before the final dungeon, Asbel gets a chance to talk to each party member separately. Each person makes physical contact with Asbel, somehow, so they also get a chance to talk to Lambda. Most of them are platonic claps on the shoulder. Cheria, the official love interest, gets a pinky swear. Richard touches Asbel's face like he's about to kiss him. And then he tries to tell Lambda something else, and we don't hear what he says. Given the situation, if it's not some variation on "protect Asbel, please," I'll eat my controller. Also, this scene, unlike all the Ho Yay-tastic skits? Utterly mandatory.
And for some Crossover Ship, Emil and Ruca are now shipped together, thanks to a scene in Radiant Mythology 3's opening where they HUG each other. Yeah, REAL subtle, Namco.
Tales Of Xillia subtly combines this with a Precocious Crush. At one point, Elise's living doll, Tipo, latches onto Milla and starts motorboating her. It's revealed later in the game that the things Tipo says and does are really Elise's innermost thoughts.