Although most of the pairings fangirls come up with have little to no basis in the anime, there's a definite argument toward 3x4. For one thing, while each pilot has their female counterpart, Trowa's is his possible sister (whether or not they're related, that's how she sees the relationship) and Quatre's is Dorothy, whom he only meets once and upon that meeting is stabbed. For another, the whole character arc between the two starting when Quatre goes crazy after his father died is proof enough.
For less sheer madness, however, there's Gundam 00, where we have the relationship between Lockon Stratos (Neil Dylandy, the original) and Tieria Erde... who are both "totally" straight as arrows! They even have private meetings where they discuss each other's feelings to prove their platonic nature. When Lockon dies, Tieria actually shows emotion due to his sheer straightness and platonic love for him. His last lines from the first season show just how much he loves girls.
Tieria:Now I can go to where you are... Lockon...
And that's not even mentioning the Foe Yay between Tieria and Ribbons.
Gundam SEED: You know what...let's just say Kira and Athrun are really upset about having to fight each other...
Dearka and Yzak too.
The anime seems to support this pairing. In episode 44, Dearka and Yzak see each other again for the first time in a while and Yzak's reaction to seeing Dearka with the Strike makes it sound like they were cheating on each other. Additionally, in opening sequences Kira appears on screen with Lacus and Athrun appears on screen with Cagali. Dearka and Yzak almost always appear on screen together in the openings.
The tendency of male characters to die tragically and serve as another male character's motive for fighting/villainy smacks of Ho Yay. Nicol and Athrun are an especially strong (and tearjerking) example of this trope.
For more old school Ho Yay, Mobile Suit Gundam provides more than enough subtext between Char Aznable and Garma Zabi that kept fans happy for more than thirty years. One includes a shower scene with a bit of coy banter; Char putting his hand on Garma while Garma's eyes glaze over, which is very similar to the look Lalah gives Char later on as he does the same thing to her; and Char killing Kycilia so she could keep Garma company in heaven, after stating to Sayla sometime before that he wasn't after revenge on the Zabis anymore. This isn't even touching on Gundam Origins, which has Ho Yay scenes between the two such as Char putting a blanket on Garma in the middle of the night when he's fast asleep on his desk. Or climbing all the way down a muddy path in the rain to pitch a tent for him until he was able to move. Does one even need to mention the scene where Char grabs a hold of Garma's hands to calm him down before they go into battle, following by an intense stare between them and sweat collecting on Garma's face?
Mobile Fighter G Gundam was bound to have this, given just how passionate everyone is. But the most prominent example has to be between Domon Kasshu and Chibodee Crockett. Not only does the Narrator continually refer to them as destined rivals, Schwarz Bruder practically matchmakes them (to improve their fighting, of course) in Guyana. And in their final battle, Domon and Chibodee actually say things like "I can feel your dream" while Master Asia says that "Chibodee has lit a fire in Domon's soul!" Clearly, they are madly in love and too dense to realize it.
Dosen't help in the song on episode 17, it's a song about friendship and love... with scenes of Asemu and Zeheart. Honestly, they weren't even TRYING to hide it.
Sei and Reiji's close and heartwarming partnership in Gundam Build Fighters can evoke this. Most of their subtext is just the side effect of a strong friendship, but some moments—such as when Sei runs down the street calling Reiji's name right after meeting him—seem intentional. Director Kenji Nagasaki also did No6, which could explain things.