Let's be honest. The Final Fantasy series always had a thing for making the protagonist's and antagonist's relationship feel... rather personal. Therefore, when you put together the ten main heroes and ten main antagonist of ten games... well, THIS happens! Awkwardness and creepiness ahoy!
And now, some of the more notorious examples are illustrated in this picture!Squall
Let's not forget Ultimecia's response to Squall's breaking through her barrage in their pre-duel cutscene:
Ultimecia: "So you would rather die hard."
Not to mention Ulty blatantly stroking his face. Sure, she had just went all ZAWARUDO! on him and was attempting to deliver a deathblow right afterward, but the fact that such an intimate gesture was the last thing she does before trying to off him...
And speaking of these two, it's probably unintentional but worth noting that the end-credits montage, which features the Heroes' cutscenes from Destiny Odyssey, has Squall and Ultimecia's scene set to a snippet of "Eyes On Me," their game's love theme.
Things get (if possible) even more unusual when Squall, the group's Team Mom, has to fight Warrior of Light, Team Dad in general. Look at it carefully and you might see a resemblance to a couple talking about how they should treat their children.
Even more apparent in 012, where Squall's intro to Bartz is "Would you stop fidgeting?" and sounds more like a mother preparing her kid for a flu shot than a combatant.
It doesn't help that he seems to be eying Terra out in the Dissidia opening and in the CGI parts of the Duodecim trailers.
His line when facing Cecil lends itself to... interpretations, both tone and line alone:
The Emperor: "Ought you not be on our side?"
And check Kuja's entry.
Moreso Minion Shipping/Unholy Matrimony than pure Foe Yay, but most fans see something going on between Mateus and Ultimecia given the sheer number of scenes in which they are seen plotting together. His Encounter line towards her in the original Dissidia suggests something of a Worthy Opponent-like relationship. As one fan best put it, "it's merely a matter of who tops."
The Emperor: "Let us crown the true master."
Cloud of Darkness
Cloud of Darkness has quite a lot of Foe Yay with everyone thanks to her husky voice, but special mention must go to her BDSM-licious response to Sephiroth:
Cloud of Darkness: "The truly mighty must be leashed."
After fighting Laguna, the former soldier gets, er... "distracted byher appearance, though not by any particular PART of her appearance," and then, after she discovers that a) Laguna doesn't see himself fit to be one of Cosmos' chosen, b) he protests that he's not taking orders from her, just helping her, and c) he desires to fight the manikins to help out his war buddies (an act that is foreseen to be—and ultimately becomes—a suicide mission), she takes a curious interest in Laguna's methodology and becomes his personal enemy for the rest of the 12th cycle, while assisting him in reaching his goal.
Dissidia 012 ramps up the Foe Yay between him and Terra to the point it rivals Cloud and Sephiroth. His comments about her sound like as an abusive parent at best and an abusive lover at worst. When she resists his control he tortures her into submission with the line "Sorry babe, I only hurt you because you make me!" When she escapes he remarks "she always comes running straight back into my arms," and he has pet names for her, including "sweetcakes" and "dame."
Then, less perverted but no less disturbing, is this gem.
Kefka: "You better straighten up missy, or I'll hafta teach you a lesson!"
ALL of Sephiroth's dialogue directed at Cloud. ALL OF IT! And it only gets creepier as it progresses.
Sephiroth: "Such a good boy! You've come back to me where you belong."
Heck, he has Foe Yay with everyone, to judge by the quote he uses after executing one of his attacks: "You look good."
And everyone certainly seems to make a big deal out of Sephiroth stealing Firion's rose, especially when you're told he's run off to the enemy's stronghold by himself because "something precious of his was stolen." (It doesn't help one bit that the guy's Japanese Fan Nickname translates to "virgin.")
And of course, the rather feminine-looking Kuja's obsession with Zidane also deserves mention. Not only does he have four encounter lines for him, but Ultimecia makes it all even creepier.
Ultimecia: "By now, Kuja should be having his way with Zidane and Bartz."
Chaos's pre-battle taunt to Sephiroth is more than a bit suggestive, seems the latter's attitude towards Cloud is contagious.
"Kneel before me if you seek comfort."
In Dissidia 012's official quests, Cecil remembers Kain since the 12th cycle was his first and thus he entered with no memories or home. It's later commented that he doesn't remember much else about home, not even Golbez (until the 13th cycle). So, Cecil awakens with no memories, and what's one of the first things he recalls? Not his wife, not his son, not his brother, but Kain. Hmmm....