Square-Enix has certainly upped their Les Yay levels in Final Fantasy XIII. Vanille and Fang care very deeply for other and they also probably have the biggest amount of lovey-dovey physical contact in the entire game. Not only does Fang like petting Vanille's head a lot more than Lulu liked petting Yuna's head, they're also the characters that hug more and more passionately through the game. Every time they talk about each other, the nature of their relationship seems pretty obvious as well. And don't get me started on the ending, where they "die" holding hands while romantic music plays in the background!
They're not really dead, they just became crystals for all of eternity. Then again, that only makes it even more romantic. ◊ I mean, just look at them.
Heck, when they finally meet each other, the game plays a romantic song and they start walking in slow motion to each other, the whole scene just screams "Oh my god they are going to kiss!" but then a random monster appears and you have to fight it...
Vanille puts her hand on Fang's breast when they hug at one point!
And then Fang kneels down and lifts up Vanille's skirt like she's completely within her rights to do so whenever she wants. Compare to Lightning who was asked to show her brand, instead of Fang just trying to unzip Lightning's blouse herself. Though Fang was not the least bit shy about seeing another woman's breasts in any case.
Fang and Vanille's dialogue with one another, at times, closely parallels that of (engaged) Snow and Serah. It could very easily be argued that the game has two central love stories.
Fang: "I'll tear down the sky if it'll save her...."
There are multiple ways to interpret Fang referring to Vanille as her "partner".
Both of their Eidolons make their first appearances when they're distraught over the idea of the other one suffering.
And speaking of Eidolons, the Shiva sisters' transformation sequence is very, uh, suggestive. They wind their legs around each other quite gracefully, locking each other into place while Snow "rides" them. Heh.
Let's put it this way; if the developers had gone with their original plan of making Fang a male character, and nothing else about the final product were different, the Fan Dumb would be complaining about how cliché Fang and Vanille's relationship is compared to previous Official Couples.
A male example: Snow and Hope. The fans call it 'Snope'
Rikku's just as bad. At least Lulu doesn't call Yuna, "Yunie"...
Rikku/Yuna gets a huge boost in X-2, with a scene where Rikku comes very close to deliberately touching Yuna's breast.
Fanservice aside, keep in mind that Rikku and Yuna are relatives. So the nickname could be more likely be seen as a loving bond between two cousins instead of themes bordering on the homoerotic.
And though they're more minor characters, Elma pretty much wants Lucil.
It's partly the result of a bad translation but this has quite a few weird Ho Yay moments, like Tidus narrating "I feel happy that Walter (Wakka) wants to arouse me," after meeting and befriending him.
And there's Rikku saying to Tidus, "Just a feeling, but I think my dad kind of likes you..."
Also, Auron and Kinoc were at the very least Heterosexual Life-Partners before Braska's pilgrimage. Kinoc's death at the hands of Seymour and facing his own killer, Yunalesca are the only times in the game Auron shows emotion. And that hug at Mushroom Rock.
The relationships between Auron, Jecht, and Braska went into this territory for at least some of the fanbase. They show a great deal of loyalty and caring towards one another, especially at the end of Braska's pilgramage. Auron's increasing desperation as they near their goal, knowing Braska will die; Jecht's willingness to sacrifice himself for their sakes; Auron's breakdown after their deaths... Auron even becomes an unsent due to his promise to Jecht to watch over Tidus, and then spends ten years in an alien, foreign land just for that purpose (though you could probably say this is out of loyalty toward Tidus, too... they did spend ten years together). He had actually planned to stay in Zanarkand indefinitely, only deciding to bring Tidus to Spira at the last minute, when Sin shows up in Zanarkand at the beginning of the game.
Tidus/Wakka seems popular for some reason.
Final Fantasy X-2 is probably the most notorious game in the series for this. The list includes:
Yuna giving Le Blanc a massage that results in orgasm sounds if she does it right
The Hot Spring scene where Rikku remarks to Yuna "I know who's got it going on". And she then proceeds to check out Paine.
Buddy getting a shirtless massage from Barkeep in previously mentioned spring.
There's about no way in hell that their relationship can be read as anything BUT incest. Strong, strong incest.
Nero: Let us become one. Let us come together, so that none may ever tear us apart. [Nero hugs him]
Weiss: Yes. Let us... Let us go join him.
For Final Fantasy IV you have Cecil and Kain. Cecil and Rosa are lovers but you would never realize that by the way the game shows it, right at the beginning, he just ignores Rosa to travel with Kain. Cecil and Kain get separated, but when you met Kain again, he is mind controled by Golbez, he got Rosa as hostage and asks you for the crystals. The way Cecil acts is really suspicious, like he is more frustated by the fact that Kain "betrayed" him than the fact that his girlfriend is a hostage. You also fight with Kain but you can't beat him despite the fact that both start at the same level and should be equally strong, Cecil just hits low or miss while Kain jumps and he deals more damage every jump until he defeats you, this lead people to believe that Cecil didn't want to hurt Kain.
There's some Terra/Celes Les Yay in VI, with Terra asking Celes (whose situation appears to be similar) if she could fall in love, and most of Celes' dialogue in the final dungeon expresses concern for what will become of Terra once Kefka is defeated and magic fades from the world.
Really this can be summed up with "It's Final Fantasy" Seriously. That alone should be your hint.
Then there's Sephiroth and Genesis in Crisis Core. Maybe it because the latter is Gackt, maybe they're just playing to the fandom now. Whatever it is, those two don't deny it.
Let's not count Sephiroth whose Ho Yay moments need a page of their own, and focus in Zack and Cloud. There is a moment where Zack undressed Cloud, in the Inn in Nibelheim. Cloud was unconscious.
And then of course there is the bridge scene in Advent Children with Reno and Rude. That is NOT the bomb they're talking about there at all.
"Ohh good! "
"You love it. I know."
"If nothing else, it's... flashy." Just the tone of voice he says it in implies it all.
The entire scene is loaded with innuendos, but it IS Reno and Rude, who are pretty much walking innuendos.
Vagrant Story (which takes place in the FFXII/FFT [universe) might as well have been called "Ho Yay: The Game". For starters, the main character spends 40 hours walking around in assless chaps.
Standard XII got in on this a bit, too. For example, one NPC is labelled as "Lovestruck Man". The first thing he ever says is about Vayne Solidor. It's not until significantly later that you learn his title is because he's crushing on a Viera bunny girl.
Final Fantasy XI has a quest where a trio of Hume npcs are accidentally splashed with a love potion. Ho Yay ensues. The potion's effects wear off just as they are about to confess their feelings, leading to a Mithran onlooker to remark with the following:
Although to be fair, it's almost exclusively from Seifer's end, as Squall denies any sort of human relationship for most of the game, and only stops being a Chaste/Celibate Hero after his Love Epiphany in Disc 3. Seifer, on the other hand, at one point in the games, imprisons Squall, puts him in a kinky position as he tortures him, all the while talking about his "romantic dream". Yeeeeeah....
The DS remake of Final Fantasy III has some of this when it comes to Arc and Prince Alus. Arc, being as effeminate as he is, forms an immediate bond with Prince Alus, and the two end up spending quite a bit of time together. They even wind up sleeping together at one point (although in seperate beds, and under the pretense of "the prince's safety"). The way they talk to each other seems to suggest that they might be more than "just good friends."
Sabin's a bodybuilder, and he is the only character whose sequence during the breakup has no female characters. In addition, his "fight" with Gau has animation quite unlike any other fight in the game but looking like something else. (Though since there are no sparkles, it can't be sex.) Apparently all the heterosexuality genes went to Chivalrous Pervert Edgar.