Vampire Knight's Kaname and Zero display mild Foe Yay, what with bloodsucking being a sex metaphor, and all.
By Vampire Knight Guilty they've added chains.
Meanwhile, Zero and his younger twin brother, Ichiru, have more Incest Subtext than you can shake a stick at.
In various flashbacks the two can be seen sharing beds, holding hands, touching foreheads, and whispering each other's names.
"I want to be one with you, Zero".
Before Love Interest Yuuki came along, Zero spent all his time wanting to protect Ichiru.
In addition, Takuma Ichijo and Senri Shiki. There is one scene in the manga, at Ichijo's birthday party, where Shiki "accidently" cuts Ichijo with the knife while attempting to cut the cake. Cue Shiki, who prefers real blood over blood tablets, commenting on how they shouldn't waste it, licking Takuma's blood off his hand. With an almost lustful expression on his face. Also, their behavior towards each other in general.
Also in a bonus manga in volume 4 Shiki is sleeping on Ichijou's shoulder.
Hanabusa has a mild Stalker with a Crush relationship with Kaname, offering Kaname his blood, getting crazy jealous of Yuuki, and defending all of Kaname's actions to the end.
In the English dub of Vampire Knight Guilty Hanabusa tells Kaname that he hated himself for not being able to admit that... "I love you, Lord Kaname!"
It should be noted here that VK fandom seems to consider Aido as being Bi the Way.
Shizuka's obsession with Yuuki.
From the moment they meet Maria and Yuuki are partial to each other, with Maria insisting on Yuuki protecting her and having no sense of personal space, and Yuuki insisting on Maria's innocence.
Maria hugs Yuuki several times and hovers near her the rest of the time.
Then there's the infamous Almost Kiss in the theme song.
Zero tells Yuuki to stay away from Maria, almost jealously.
On top of all this, if you look closely there's a guy in line to give Kaname chocolates in the Valentines Day chapter.