The Kingdom Hearts series, especially the second game on the PS2 (in particular, watch when Sora gets on his knees for Riku. He doesn't cry when he finds Kairi again, but when he finds Riku, he breaks.), is full with Ho Yay undertones between Sora and Riku.
You can watch the whole scene here (SPOILERS). When Sora finds Riku he drops to his knees HOLDING HIS HAND, almost crying! "Oh I looked everywhere for you!" Now, when Sora finds Kairi, he just greets her and then she throws herself on his arms. What does Sora do? He gives an awkward and hesitant hug.
In the first game's intro, the lyrics "Don't get me wrong I love you" play with Sora and Riku on screen.
In the early part of the game, there's a scene in which Riku hands Sora a paopu fruit and explains to him that when two people share such a thing it entwines their destinies. He finishes this with: "Come on, I know you want to try it." Kairi's name is not mentioned at all in this scene, so if you take it out of context it comes across as Riku asking Sora to share a paopu fruit with him. Erm...
Also in the first game, Riku gets pretty mad when he thinks Sora has "dumped" him for Donald and Goofy. Sure, it's technically a friendship thing, but there are some who look at it differently...
But even they pale in comparison to Axel and Roxas' subtext-that-might-as-well-be-text in Kingdom Hearts II and 358/2 Days (very chiefly on Axel's part in both cases, as Roxas is shown to be too naive to fully grasp the idea of love). Then there's the hintings of Axel having some kind of deep relationship with Saix before they both become Nobodies. Axel will do anything to save Roxas in KH2, even going against the Organization and performing a suicide attack to save him.
Not just that—Axel by all accounts goes completely bonkers when he realizes Roxas has become Sora and doesn't remember him.
One of the bonus scenes in the Japanese-only Kingdom Hearts 2: Final Mix, in which Axel and Roxas' spirits meet up one last time on the clock tower after Axel's death, where Axel questions the fact that they're not supposed to have hearts, and seems absolutely heartbroken that this will be the last time he can ever see Roxas. When they say goodbye for the last time, Axel addresses Roxas by the Japanese word for partner, and a single tear falls from his eyes.
Sora: Axel? What were you trying to do? Axel: I wanted to see Roxas. He was the only one I liked. He made me feel...like I had a heart.
Or how about this one:
Roxas: No one would miss me. Axel: That's not true! (quietly) I would...
To say nothing of the fact that the first thing Axel does when he's realized that Roxas has become Sora is to track down Sora's girlfriend and kidnap her, complete with very loaded dialogue. It's strongly implied by Axel's last words that he was planning on using Kairi to transform Sora into a Heartless, and thus release Roxas again.
Axel: We've got something in common, Kairi. You and I both miss someone we care about.
Oh, and then there's Seifer's "Isn't this ROMANTIC!?" line, in battle against Roxas or Sora. Although the line could be a reference to his Final Fantasy VIII counterpart.
Terra and Ven in Birth By Sleep also qualify here, especially from Ven's side.
Probably the biggest amount of consistent Ho Yay, (throughout the Re: Chain Of Memories, and with the most questionable dialogue,) was between Sora and Replica Riku. Repliku kept acting like some sort of heart broken lover in regards to Sora, using phrases like, "You never cared about me!" and "You're only ever worried about her!" It's a big Flanderization of Riku's Foe Yay with Sora in the first game. The pinacle of this pure Yaoi Fodder was this little exchange.
Repliku: Sora... You're always trying to worm your way into my heart! Sora: Hold on...When did I ever do that? Repliku: Oh, so you forgot about THAT too?! You never cared...IT NEVER MATTERED TO YOU! (runs off, might as well be crying angry tears.)
Aqua in Birth by Sleep manages to have this with Cinderella, by taking the man's place in the scene where, in the movie, the Duke takes her hand and guides her to a chair. Then by shielding her with her body when they're attacked. Then by helping her up with a lingering hand on her ass. Watch 2:06, and from 4:03 to 4:25 if you don't believe me.
The Ho Yay continues in Dream Drop Distance, as Riku subconsciously dives into Sora's dreams to protect him from darkness's influence. Doesn't help that the two constantly reference each other.
Some of Mickey's comments add to this:
Mickey: It’s like each of you is holding on to a little part of the other.
Mickey: Riku and Sora. The Sound Ideas you set free joined together.
Let's face it, 3D really played up Sora and Riku's "bromance" for all it was worth. Especially Riku's speech before he dives into Sora's dream the second time.
Riku is a Dream Eater for Sora. How do you make Dream Eaters stronger? By petting and...ahem...rubbing them.
Lea's first thought after he wakes up is understandably "Where...what happened to me?" His second thought, though, is "Roxas?" Priorities, everyone.
YMX seems quite amused/pleased at the thought of Sora thinking he is part of Sora's dream, and right before Sora falls into a coma from submitting to the darkness he leans in rather suggestively... Heck, that scene has rape-y tones in general.