Yuma and Astral, also called Keyshipping, complete with tentacle porn (thanks No. 96).
The first Japanese opening even seems to promote the paring.
Episode 97 has Astral go yandere.
Episode 98 has the first time they touch. Also when Yuma finds Astral inside the giant Astral statue, Astral says lines that make him come off as a heartbroken lover upon realizing that his partner cheated on him behind his back.
Yuma and Shark (pairing name Sharkbaitshipping) have been showing this off practically since Episode 10, but 61 and 62 pretty much cement it, as Yuma can't decide who to save between Astral and Shark when given the choice, and Shark mentions that it was Yuma's heart that saved him from Tron.
Yuma: Even if I were to win, it would feel much worse losing you!
At the end of Episode 83, Yuma is about to fall down a crevasse, and despite Kotori (who would seem more likely to save him) and Kaito (who was better equipped to save him) being there, Shark is the one who throws himself forward to catch Yuma as he falls...resulting in them both falling and ending up in hospital.
Episode 84 is essentially a tribute to the pairing, as after Shark goes out of his way to snap Yuma out of his Heroic BSOD and Astral points out that Shark lost the duel on purpose, Yuma tears up...and tries to hug Shark. The episode ends with a highly appropriate rainbow in the background as Shark pushes Yuma's face away from him (because that's clearly what you should be worrying about when someone's apparently trying to hug you).
During episode 85, Rio warns Shark and Kotori that Yuma is in danger, and while Rio and Kotori take the much more reasonable ground entrance to save Yuma (and Rei), Shark shouts Yuma's name and dramatically leaps off the top of a shipping container to land between Yuma and the Barian brainwashed students surrounding him. Yes, Shark, because that was entirely necessary.
Shark and Number 32: Shark Drake. No really throughout season 3, Shark Drake tried many times to control Shark including using words such as "Accept me, and free the darkness within you...! If you want to win, accept me!" and "Become one with me" not unlike Yubel, each time becoming more difficult for Shark to resist, despite his constant rejections. Shark finally gave in and allowed Shark Drake to feed off his emotions, at the same time we see a mental image of Shark Drake "swimming" towards Shark. Shark Drake pretty gave up after Shark's duel with Yuma, yet it still remains with him. Tron's insistence in Shark using it sounded more like motivating two lovers to get closer together.
Tron: (to Shark) "Shark Drake desires you..."
Not to mention he was this◊ close to him while saying the above quotes.
When Shark Drake first try to possess Shark, he touched him on the chest.
Episode 22 basically triggered the entire Challengeshipping (Kaito/Shark) fandom with one line; "You're quite the romantic/romanticist." Of course, Kaito was referring to the historical period, but the fandom thought otherwise.
The Dilateshippers (Kaito/V) were already fairly rampant when they found out about Kaito and V's previous relationship with each other, but episodes 55 and 56 layered on the subtext so thickly that it practically just became text.
Kaito: Ever since that day, somewhere in my heart, I've been chasing you all along.
Episode 72 got the Photonshippers (Yuma/Kaito) going; when trying to explain the excitement of duels to Kaito, Yuma uses the phrase "Kokoro no doki doki," loosely translating to "makes my heart beat fast". However, the term is also used to describe the feeling of falling in love with somebody. Kaito then repeats it back in an extremely confused tone, which only makes it worse.
The mere appearance of Rei Shingetsu in Episode 76 has sent the fandom wild with Rei/Yuma shippers (the consensus on the pairing name seems to be Positiveshipping); not surprising considering his introduction involves him tripping over Yuma and ending up in a rather compromising position◊ with him. Which Rei seems remarkably cool with. And then it turns out he's a Yuma fanboy. Is it any wonder the fandom latched onto this?
And then in episode 80, Yuma finds a letter on his desk which is slightly misspelled - and Rei promptly pops up from under his desk to assist in reading it. Understandably, Yuma freaks out and asks him what he's doing there.
Rei: Heh...I'm just meaning well.
It starts to get a bit ridiculous in 85, when Rei is brainwashed and grabs Yuma from behind, pressing his face into his shoulder for a second before apologising and saying he "only means well" in a ridiculously quiet, creepy voice. We then get a shot of Yuma trying to reason with him while Rei is wearing an impressive Slasher Smile, still holding Yuma.
Epsiode 87 is mostly all about Rei and Yuma's relationship; there's a heavy focus on how similar the two are and how they trust each other, and both get rather broody when the other betrays their trust in a way (when Gilag tells Yuma that Rei attacked Alit, and when Rei realises Yuma didn't tell him about the fact that Gilag wanted to duel both of them, not just Yuma). We end up with what amounts to a face-to-face confrontation with Rei in tears, asking Yuma...well:
Rei: So you can't trust me? Is it because you don't need me?
Epsiode 88 basically hinges on their desire to protect each other, making it rather bromance-filled, to say the least.
And then in episode 92, one of them decides that the least suspicious place they can possibly meet for a serious, private discussion is...a cubicle in the boys' toilets. Together.
With episode 95, parallels can be drawn to GX season 3, with all Ho Yay from it intact.
By episode 96 though, it quickly becomes No Yay when it turns out that Rei was actually Vector.
One of Astral's lines in episode 97, "You left me for him, Yuma..." with "him" referring to Rei/Vector, can be taken in several questionable ways.
Near the end of episode 80 Alit imagines Yuma as a Angel and as a giant head over the earth just as he did with Kotori earlier in the episode. Also crosses into Foe Yay considering Alit is a Barian Lord.
In episode 85 Alit essentially defects from the Barian side simply because he wants to duel Yuma again.
We also have Gilag and Alit, who probably get along the best with each other as opposed to any of the other Barians. Gilag gives Alit romantic advice, Alit talks about his problems to Gilag...it's fairly bromance-filled, even before Gilag swears revenge on the person who attacked Alit.
Gilag: I'll be getting revenge for Alit. It's gotta be me.