In Episode Two, both Jack and Yuusei are looking up at the moon and thinking of each other.
The English dub doesn't help in this regard either. Right off the bat, the Hyper Drive opening has only alternating shots of Yuusei and Jack to romantic lyrics like "I can hear you breathing, I can see you coming!". Qualifies as both Ho Yay and Getting Crap Past the Radar.
If you assume other countries would try to iron out those Double Entendre-lines, you're wrong. In the German version, Mr. Armstrong/Takasu even calls Yuusei "Süßer", which means "Cutie". And that isn't the only weird case of innuendo that was inserted by the German Dub. Added to all the subtext of the American version that made it through translation, this is one nice amount of Ho Yay. Really, at this point you wonder why they don't just drop the pretense of 'subtext' and be done with it.
Ushio specifically states in the English version of episode 11 that he thinks Yuusei is starting to like him.
Hell, Pretty much every single male character and Yuusei. Even The Guys Want Yuusei. He's been hit on blatantly by Yanagi and is flirted with by his cellmate, Aoyama. This troper would also argue that Crow gets awfully touchy-feely with Yuusei, given that they haven't seen each other in only the writers know how long. Rua also jumps on Yuusei after he defeats Jean.
Speaking of the English dub, Crow suggests in episode 31 that Yuusei and him should get a room together, in prison. This troper just wonders which of them would have dropped the soap.
Team Satisfaction (known in the English dub as "The Enforcers"). As we see in episodes 33 and 34, it's composed of attractive teenage guys who go around "satisfying" themselves. It speaks for itself. Mind you, they do this by handcuffing people. HANDCUFFING people. And then dueling them into submission.
Episode 55 features Kiryu dying in Yuusei's arms amid a shower of shoujo sparkles.
Even more blatant considering how similar it is to Carly dying in Jack's arms a few episodes later.
There's also some Incest Subtext between Rex and Rudger. Episode 64 comes to mind... even people who don't ship it have had to admit to the vibes.
Potential Ho Yay is lampshaded at one point when Rua uses a phrase to describe Yuusei and Bruno that, according to his sister, is usually used for describing couples. Amusingly, this gets Aki up in a huff.
Crow and Jack spend a lot of the third Story Arc "bickering like an old married couple," to borrow the colloquialism, with Crow constantly yelling at Jack to get a job and stop wasting their money. There's also the scene in Episode 79 where Crow suddenly gets jealous when Jack talks about how much Yuusei means to him as his best friend and rival. So we officially have a Bromance Love Triangle in the works.
Let's face it, one could write a book on the Ho Yay between Jack and Crow.
Jack constantly gets jealous over Yusei paying attention to somebody else. You can regularly see him pouting in the background, eyeing the potential competitor suspiciously and, in the case of Bruno, even beating them up if they get too close to Yuusei.
Ah, and we can't forget episode 84 when Jack was framed for a crime he didn't do...blah, blah. During a duel, he proudly exclaims that he duels for what's right and he's not the old Jack he used to be. He also says that he's stronger than he used to be because he has people in his life that he trusts *camera switch over to Yusei* and loves at which point the camera lingers tellingly on Crow while a distraught Carly exclaims, "Who me?" in a small bubble in the background. Make of that what you will.
Right before that, in episode 83, when Jack is imprisoned, Crow argues very passionately with him and has to be restrained by Yuusei. It's easy to view the scene as intimate.
Episode 145 breaks the Ho Yay meter. Antinomy a.k.a. Bruno, rams Yuusei's D-Wheel from behind to push him out of the black hole in an intense scene. The episode ends with Yuusei mourning Bruno/Antinomy's death similar to how he mourned Kiryu's temporary death in episode 55.
It doesn't help that Antinomy's D-Wheel is pretty phallic.
In episode 150, when Yuusei thinks about all the members of Team 5Ds and in episode 151, when he remembers everybody he encountered over the course of the series, Bruno just happens to be the last person who appears both times. Bruno also happens to get the most attention both times, where he gets to mentally converse with and smile meaningfully at Yuusei (respectively) while everyone else gets a quick still shot. Make of that what you will.
For the elusiveLes Yay, Sherry winking at Aki and Aki blushing. 4Kids left it unedited.
Carly, Mikage, and Stephanie's rather "close" relationship for rivals-in-love qualifies too. At one point, Carly cups Stephanie's face and tells Jack not to make this "cute girl" sad.
They could have made it out-and-out lesbianism, but it was easier to just have Carly blushing while Misty leaned into her personal space and told her what a pretty face she had.
The part where Carly visits Misty at her apartment. They were really happy to see each other and they seem to go on a date, with Misty's female servant looking on with jealousy.
Let's not forget their "hug" at the top of the Arcadia Movement building.
Misty and Aki definitely count as well, after what happened between them in episode 61...