Akito's relationship with Ikki is this all over. For example, Akito once kissed Ikki full on the mouth and often tries to kiss, bathe, and sleep next to or with Ikki, and constantly has No Sense of Personal Space around him. And after "rescuing" Akito, Ikki lets him stay at his house, and the only thing in any of this he seems to have a problem with is Akito's tendency to kiss him. Akito's also apparently fond of crossdressing and is even shown to have a dark side of his own, becoming jealous to the point of scaring Kururu when she gets too close to Ikki.
Ikki and Kazu's relationship. Despite feeling inferior to Ikki in terms of ability, Kazu is fiercely loyal to him and often shows that he values Ikki's pride and well-being far beyond his own. For example, prior to Ats, Ikki had become the new leader of the East Side Gunz, but he abandoned this position to pursue his future in Ats. The former leaders of the Gunz offered Kazu the prestigious leadership spot of the Gunz in exchange for Kazu providing them with Ikki's head. In reply, Kazu fought all five of them at once; instinctively sticking up for Ikki.
There's also Yasuyoshi Sano, the Aeon Clock, who is shown to be homosexual and flirts with a few guys, though he is shown to have a particularly strong attraction to Ikki, once confessing his love for him by saying that his life is Ikki's "feathers" and that his "heart is still inside those wings engraved with the same time".
Then there's this little number:
(Aeon just made Ikki fall asleep with Incense, making Agito question why)
Agito: "What's this?"
Aeon: "Well... With all the colossal battles we've been having lately, Itsuki-sama seems very fatigued... it's only natural. I thought that a restful sleep would do wonders, that's all."
Agito: "THEN WHY THE F*** ARE YOUR PANTS GONE??!!"
Aeon: "OH S*** !!!!"
After that there's the scene where Akito strips from the waist down and offers to take Ikki's place for Aeon.
Sano also seems to share a bit of Ho Yay/Foe Yay with Spitfire, although it's msotly one sided on his part
Agito and Ikki have a bit as well, but not all that much compared to the rest of the examples.
Kilik was known to have a very close bond◊ with Sora when they were friends. Rika even states that "compared to everybody else those two are different". Not to mention the reversed tattoo on their backs◊, which display a word "飛地" literally meaning "enclave", "narrow range" or "inner circle".
Shalott and Arthur; they're in an explicit and mutual homosexual relationship.
Buccha and Orca. They became extremely good friends after their fight, with Orca doing everything with Buccha. In the final shot of the team, you can even see Orca riding in Buccha's pants like a baby Kangaroo in its mother's pouch.
And now for some Les Yay. Kururu asks how Ringo can carry money in her Croissant Mask costume, and Ringo shows her some money in her cleavage. Kururu immediately compliments said cleavage.