In a series chock-full of Ho Yay, Hishigi and Fubuki may take the top spot. Let's go down the list, shall we?
Their first interaction includes this line from Hishigi:
Hishigi: I swore to follow you until the end, even if that path carries us both to hell.
When Hishigi is Driven to Suicide after implanting the Devil Eyes, Fubuki hauls him to his feet by the front of his shirt and says that Hishigi is not allowed to die until Fubuki says he can.
Before Muramasa's departure from the Mibu, he told Hishigi, "take care of Fubuki for me."
Just before stabbing himself in the heart in order to activate the secret technique of the Taishiro, Fubuki tells Hishigi, "You have my thanks for standing by me all these years. I wish you to live until the end."
Hishigi's death scene. He has taken several of Kyo's most powerful attacks in attempts to shield Fubuki. The Devil Eyes have been destroyed, leaving him extremely weak and dying. But when Akari mentions Fubuki, he manages to get to his feet and attempt a Taking You with Me with Kyo. When that doesn't work and his body starts dissolving, he staggers to Fubuki and rips out his own heart, implanting it in Fubuki so that he can continue living after destroying his own. In the original, he says that he will live on with Fubuki. In the English translation, he has a speech about how he chose his own path and says "I hope you can find the heart to forgive me...for leaving you all alone." He then disintegrates in Fubuki's arms.
Yukimura says outright that he loves Kyo at one point. Then again, pretty much everyone loves Kyo.
Akira has a massive man crush on Kyo, starting around the age of ten.
Hishigi once tells Kyo that he has beautiful eyes, while touching his face. Hishigi's not even trying to dispel the rumors. Of course, it's entirely possible and pretty heavily implied that Hishigi actually is gay, and just about everyone flirts with Kyo at some point.
During his fight with Tokito and before he finds out that Samus Is a Girl, Akira says that Tokito has "a sweet face, which hides the wretched coldness of your heart."
Saizo's Bodyguard Crush on Yukimura (even more blatant in the anime than in the manga, which is impressive) is played for laughs on a regular basis.
Yukimura also has some with Shindara, also known as the original Sarutobi Sasuke, who was once his most trusted soldier.
Played for laughs with Akari, who is physically male, but her gender is accepted enough to be another woman in Kyo's eyes. He has promised to marry her if she ever lands a hit on his face.