From Psyren, Oboro likes Ageha. A lot. He has the ability to cure people of their injuries by hugging them close and when he was curing a injured Hiryu he stated that he didn't like doing so because it was boring, and that he would rather cure Ageha because he likes him, stating that if Ageha got hurt, he would "hug him any time".
And immediately after Oboro gets infected with the Psyren disease he hugs Ageha close and breaths heavily on his neck. Ageha freaks out and tells him to get off, and Oboro tells him to bear with it since he's feeling sick.
There's also Sakurako's obsessive infatuation with Matsuri. Also, Matsuri openly gropes Sakurako at one point.
Some Ho Yay could also be argued for the Kyle/Ageha relationship. He initially sees Ageha as a threat but after being defeated by him considers him to be the big brother he never had and idolizes him. He gets really happy whenever Ageha comes to visit/train at Elmore Wood and upon seeing a battered Ageha in the future, promptly hugs him◊ with a sad expression on his face and glomps him later on.
One of the reasons Eiji is following Miroku is because "you're better looking than me". He's also hesitant in fighting Shao because it would "be a waste to kill such a good looking guy".
Fredrica is very fond of her friend Marie to the point of being overprotective, and beats up anyone if she suspects they badmouthed Marie.
Also, Mithra towards Marie in chapter 131.
Miroku and Grana are always throwing secret smiles to one another.
And then there's Hiryuu and Tatsuo. Don't forget that Hiryuu went to Psyren only for this one friend. Their history together plays out almost like a childhood romance. To explain, Tatsuo was always sick, and admired the "tough" and "cool" Hiryuu... who was actually a crybaby and indeed lied to Tatsuo about being that way, but only to cheer him up by telling him great stories. And when Tatsuo was down, Hiryuu promised him that they will be a team of one dragon, with Hiryuu as the brawns and Tatsuo as the brain. When they were forced to part, Tatsuo gave Hiryuu a pendant that showed exactly that, and Hiryuu kept that pendant. So Tatsuo was Hiryuu's reason for becoming stronger, because he wanted to "face him with pride the next time", making that promise and the lies true. And Tatsuo's reason for going to Psyren was solely Hiryuu, because he wanted to be a hero like him. Then we have the very Ho Yay-ish "I Know You're in There Somewhere" Fight, where Hiryuu hugs Tatsuo very close and tells him that he's not alone and that he'll be right there. The all blacked out drawing on this page however makes the hug look morelike a kiss. And after Tatsuo'sBig Damn Heroes moment, Hiryuu stays with him in Psyren.