From the get go, "07-Ghost" was loaded with Ho Yay between Teito and Mikage- Only halfway through the first episode, they slept in the same bed, and this was merely the beginning of it.
The manga version is chock full of Ho Yay. In fact, when Mikage and Teito meet again in the 7th district, Frau queries the following: "...Is that his boyfriend?" Then there's Teito and Hakuren's holding hands... And Teito's Foe Yay with Ayanami... And Shuri's sparkles around Konatsu... And then some.
Ayanami/Hyuuga. What with Hyuuga being incredibly loyal to Ayanami, pretty much always being by his side, protecting him, calling him "Aya-tan!", and making it clear that he will absolutely not tolerate anyone trying to either harm or insult Ayanami.
On the subject of Teito and Mikage: Despite the fact that his closeness with Teito makes him a target of ill will, he remains a bright and cheerful person, sticking with Teito even if others make fun of him. As well as both of them making a point to stick up for the other against bullies or saving one another from danger. Their relationship as friends involves a lot of Mikage teasing Teito about his short stature, and Teito beating him up in retaliation. Even so, they are still very close, promising each other that they will die together and will always be "the best of friends". And Mikage often tries to get Teito to loosen up, telling him that if he smiles and laughs more, he'll grow taller.
Since the events of episode 1, Teito and Mikage have been separated and are shown to miss each other terribly, constantly thinking about one another, and Teito trying his hardest to escape the church he's staying at and make it back to Mikage. In ep 4, Teito meets with a demon (otherwise known as a "Kor") disguised as an old man offering to grant him his hearts desire at the cost of his soul. Hearing this, Teito tears up and instead of say, wishing the guys who are after him would drop dead, or to bring his parents back to life, he only wishes to see Mikage again. And after Mikage helped Teito escape he is captured and brutally questioned by Ayanami and Hyuuga on Teito's whereabouts. When he refuses to cooperate they give him a Sadistic Choice of ratting out Teito's whereabouts, or giving up his family. He decides to give up his family under the pretense that "they would understand" that he could never betray his best friend. In ep 4 when he decides this, he and Teito are given a split screen to show a speech they give completely in unison about how they'll never abandon one another. And then they do a fist bump.
When they are finally reunited again Mikage is shown looking extremely relieved and rushes towards Teito. A flying glomp, coupled with some sparkles, ensues. Hell, Mikage even tells Teito that he considers him to be as important as his own family before declaring "I love you, Teito."
After his death, Teito still finds it hard to go on without his best friend, even stating that "When Mikage died... I felt like a part of me died as well". When Mikage's soul is taken by Ayanami and he dies, he begs Teito not to look for revenge, but instead to keep walking towards the light. This shakes Teito's beliefs, because Mikage was his 'light'. Later, Mikage becomes reincarnated as a small pink dragon (called Burupya) because he wished to protect Teito, no matter what form. Even after his death, Teito still cares about Mikage very much; when Teito is struggling with learning how to use the Bascules, Bastien tells him that he needs to think of his feelings for God in his heart. Teito then thinks "Though I don't really know anything about God, I'm thinking of you... Mikage."
Teito and Frau have their fair share as well.
For example: Although Frau is quite the ladies man, flirting with girls and regularly looking at porn, his relationship with Teito is a bit questionable. He enjoys teasing and annoying Teito about how he looks like a small child, and for all his teasing, he also keeps Teito's spirits up with impromptu pep-talks. And despite Frau's tough looks and rough exterior, he is actually very caring and cares very much for Teito, showing some hints like protecting him from danger and carrying him bridal style. He also says that his meeting with Teito for the first time is not a coincidence but that it actually was fated for them both to meet and considers Teito to be a "shining ray" in his life.
Frau: (To Teito) "I like your soul so I wouldn't mind dying by your hands if I had to."
How about when Teito gets a "promise collar" put on him by Ayanami, which is accidentally activated by Frau and the fact that the collar has to hear Frau's voice at least once a day, or it will explode?
There's also that scarf Teito intentionally buys for Frau (in the manga during the Capella arc). However, he gave it to a homeless person instead.
In the anime, the sheer number of times Teito blushes when he is with Frau is quite surprising.
There's also the fact that Teito tends to act like a Tsundere around Frau.
This scene. You got Frau whispering into Teito's ear "If you want to put me at ease, smile", Teito blushing in response and then forcing a smile.
In the anime there's also a scene where Frau hugs Teito close to him and says "I know what's important, and its not the eye."
This scene (read on for another 4 pages) just drips with ho yay, having Teito declare that Frau is alive "in his world." Frau ruins the mood by shrugging it off, but he's clearly pleased if his smile is any indication.
Kuroyuri and Haruse. There's even an off-screen "kiss", in which Kuroyuri bites his lip to give blood to an injured Haruse. Of course, Kuroyuri is a character of Ambiguous Gender.
Castor/Labrador. Castor tends to act somewhat protective of Labrador, constantly speaking in his shoes, stating that his prophesies always come true. The two are usually seen together, especially in the manga.
Castor saved Labrador from Ayanami's grasp when he tried to devour him in order to get Profe's fragments, causing him to lose his left arm and eye. After meeting up with Teito and Frau, Labrador wore women's clothing and pretended to be Castor's wife when infiltrating Ouka's birthday party. The two were also trapped in a "Ghost-Proof Cage" for quite some time together.
And of course the Ho Yay between Teito and Hakuren was not at all reduced by Hakuren's statement that he doesn't like women (well, with a few exceptions, but...)
Major Teito/Hakuren moment here. Bonus: The scene takes place in Frau's bedroom.
Hakuren blushes when, for the first time, Teito openly acknowledges that they are friends. There's also a scene where he stares at Teito when Teito's taking off his shirt. Granted, Hakuren was staring because he had just noticed Teito's sklave tattoo for the first time, but still.
On the cover page of a manga chapter, Hakuren and Teito are shown bathing together in a rather small bathtub.
Before Ouka's birthday party, Hakuren and Teito practise dancing together, and Teito dips Hakuren.
Then there's the Eye of Mikhail, which refers to Teito as being one of its most beautiful masters, and later personally tells Teito that it loves him more than anyone else does. It's also rather possessive of Teito and doesn't let anyone it's not comfortable with to touch him.
That bit of Foe Yay with Ayanami and Teito. In the minidrama "Escape," Ayanami is featured crossing paths with Teito and Frau, "making a serious love call" (as Frau jealously puts it), declaring how he and Teito "cannot live without the other" after a process of quiz show fanfare.
In a manga chapter, Ayanami called Teito "my possession".
And then there's Dattebayo's fakesub. (On the downloads page as "07-Ghost 26")
Ayanami/Yukikaze. What with Hyuuga saying that Ayanami and Yukikaze were 'practically married', and Ayanami's impassioned speech about Yukikaze being 'beautiful under Cherry Blossom petals'...yeah. Also, consider that Yukikaze's death reminded Ayanami of Eve's death, Ayanami is Verloren's reincarnation, and Eve is Verloren's canonical love interest.
When greeting Mikhail in chapter 86, Raphael curtseys, blushes and is surrounded by hearts.
Hyuuga/Konatsu. In the 5th Limited Animate DVD, Hyuuga is referred to as Konatsu's 'husband', and Konatsu says that he loves Hyuuga, adding: "As the sun rises in the east, it's (loving Hyuuga's) a matter of common sense."
Castor/Teito. Castor has shown numerous times to be rather protective of Teito, including making a point to have his dolls keep an eye on him, comforting him when he's upset, and giving Frau a stern reprimanding or whack to the head whenever he catches Frau teasing or making fun of Teito.
There's that time when Labrador gave Teito a purple rose which is supposed to be a good luck charm, and according to Castor, it's called a 'Silver Rose' or 'Flower of Protection'. And then Frau picks up Teito bridal style to take him to dinner and Castor picks up the purple rose that Teito had dropped and places it in Teito's hair.
Labrador's foster brother called him "my most precious treasure in the world".
There's a bit of subtext in Mikhail's and Frau's relationship. They argue a lot but also willingly share responsibility for protecting Teito, and appear together in official art fairly often.