Monochrome Factor: Taken Up to Eleven in the anime, which pushes this between Akira and Shirogane from the very first episode and every episode afterwards. Kengo is also shown to be attracted to Akira, and Kou flirts with anime-only character Haruka on more than one occasion.
Haruka blushed upon looking at Akira in the first episode too.
In the fourth episode Kengo hugs Akira from behind and when told that he can't fight Kokuchi with Akira and Shirogane he says he doesn't care about fighting Kokuchi he "just wanted to be with Akira".
In the sixth episode Haruka says of Shirogane "Since the time Akira-kun's hair color changed to black, I've seen an unbelievably beautiful person in front of me."
Episode 7: Shou who's actually a girl is in love with Mayu, Kengo's older sister. And Ruru tells Shou "If you really like girls why don't you have a relationship with me?"
Episode 8: Akira plays Hamlet in a school play and Maki, another guy plays Ophelia. Hamlet and Ophelia have to kiss at the end of the play. Not to mention how Shirogane acts very troubled when he learns that Akira has to kiss Maki.
Episode 13: Kou hugs Kengo and Akira with sparkles in the background, flirts with Haruka a few times, jokingly flirts with an old man, and says that he and Shirogane are having a secret affair. At the end of the episode he also kneels before Akira and says "Until death. Until I rot away, I will stay by your side. My King."
Episode 16: Kengo has a mental image of Akira naked and Kou and Shirogane say they want to see Akira naked.
Episode 17: After seeing Akira win a boxing match Kengo is seen with a heart in the background while blushing and saying "Akira, I fell in love with you again!"
Episode 18: Shirogane glomping Akira three times and asking him while getting close to his face "You were dreaming about me weren't you? Then let's keep dreaming..." Later he tells him "I will always be by your side Akira-kun" while taking a bath with him and blushing. And he sleeps with him too. Akira gets jealous upon seeing Shirogane with Ruru and a girl named Kanzaki is shown to have been in love with Aya. Not to mention that Kengo tells Kanzaki that he understands her feelings of love towards Aya and is shown to immediately think of Akira. And at the end Shirogane tells Akira "Don't worry. I won't make out with anyone besides you."
Episode 19: Shirogane gets jealous upon learning that Mayu has taken a bath with Akira in the past.
Episode 20: Kou hugs Haruka and calls him beautiful. Shirogane sees Akira in a butler outfit and states "Akira-kun, it fits you well. Just once I'd love for Akira-kun to dress like that for me."
Episode 21: Shirogane tries to sit closer to Akira but Akira pushes him away. Also, Kou and Andrew. And Shirogane sits close to Akira and asks him if he thinks he's beautiful.
Episode 22: Shirogane says he loves Akira and tries to kiss him.
In another episode Shirogane says he wants to be alone naked together with Akira, states "I'm only interested in Akira-kun's naked body" and gets real excited when he sees Kengo naked.
Episode 24: Shirogane says that he loves Akira "so much". Akira x Haruka with Akira doing everything in his power to save Haruka and hugging Haruka close to his body. Also, Akira kisses Shirogane and they try to hold hands before Shirogane disappears.
The manga has its fair share too, including but not limited to:
Akira's bizarre mental image of Kengo dancing naked. A mental image that he seems way too interested in.
In Lulu's debut, Aya is who she chooses to focus on (along with her breasts).
After Lulu's Heel-Face Turn, she and Aya divert into almost Schoolgirl Lesbians territory. It's mostly one-sided, and Aya seems more weirded out than anything else, but then you get that nice splash page of the two of them naked, breasts smooshed together...
Sawaki telling Kou that if he can defeat him, he'll gladly "follow him to the depths of hell."
Kou and Kengo have some as well, especially during◊ this◊ intense◊ fight◊ in which Kengo looks more than flustered when Kou is "sucking the darkness" out of him.
All that cutesy Shirogane/Akira subtext in the anime suddenly becomes very darkly ironic with the revelation in the current arc of the manga that Shirogane has been using Akira and everyone else this whole time out of desperation to revive Ryuuko. So I guess we can say that this is subverted and played straight at the same time?
Homurabi's entire motivation for killing Ryuuko, banishing Shirogane and throwing the entire world out of balance was just so Shisui, his counterpart, wouldn't be replaced. If that isn't subtexty, I don't know what is.
Don't forget Akira's whole thought process while fighting a kokokuchi- possessed Kengo. Come on, it's slightly subtexty.
Not to mention Akira's reaction when he he'd to apologize to Kengo after the whole '"not my friend" fiasco. That expression and the way he acted wouldn't have looked out of place on a violent tsundere person about to apologize to the person they have a crush on, only to bail out at the very last minute.
Also, 'HOW DARE YOU LET SOMEONE ELSE CONTROL YOU WITHOUT MY PERMISSON!!!' Seriously, he sounded like a possessive wife over her husband! Although he was really, REALLY angry at that time...
Also, the reason he was so against Kengo joining in at first. Not really sure if it can be considered as Ho Yay, but... Awww...