The most understated pairing in YYH is Kazuma Kuwabara and Yuusuke Urameshi. From the premonition of a kiss, to one or the other going full-blown hysterical whenever they other is hurt—except in the instances when they are hurting one another. They are the quintessential guys who hate each other becoming best friends. The focus is definitely on Yuusuke's emotional outbursts increasing his reiki and it's usually Kuwabara who is the one who has to get injured in a big way for him to peak.
More acknowledged is Hiei and Kurama. Though both tend to be introverts on the show, Kurama is the only one that Hiei appears to trust completely, even showing up at Kurama's human home more often than not. Also, Kurama mentions whenever they're fighting Sensui that "this might be the first time Hiei has ever been willing to die for anyone other than himself". This is actually untrue because when Kurama was knocked out after his fight with Touya, Hiei almost released the Dragon of the Darkness Flame whenever Kurama was being thrown around while unconscious even though it meant that he would die at the time since he hadn't mastered it yet. Kurama was unconscious so he never knew he was about to do that. One is rarely seen without the other, and there is promotional art for the series where Kurama is hugging Hiei (the fact that he can do this and live says something right there) and one where he has his arm around him in a very possessive manner. Most of the official art shows Hiei and Kurama together.
One thing you will notice is that they hint towards Hiei and Mukuro only in the anime. The whole scene with Hiei falling into Mukuro's arms never happened in the manga. Neither did the scene where Kurama tells Hiei he's not interested in him. It's rumored these were added to ward off suspicions of them being together.
Considering the "birthday present" Hiei gives Mukuro in the manga and the fact that he remains with her the above is just speculation.
Wait, when did they confirm the two knowing each other in the Makai? The Maya side-story confirmed that Kurama at least knew Hiei's reputation, but it was made pretty clear that they didn't actually know each other. Plus half the story is about Kurama not being able to admit he loves this girl for whatever reason.
Well it's not really confirmed that he loved her. The reason he could obviously never be with her (and honestly why would he want to) is because he hadn't planned on staying a human at all. He still really doesn't. When it comes down to it, he's a demon and that's all there is to it. Also I think they've both heard of each other but I don't think they had a past together specifically. I'll take the liberty of removing whoever put that.
Yusuke touches Kurama a lot and Kurama never seems to mind. He also has the most obvious, freaked-out reaction during the Dark Tournament in battles whenever Kurama's Batman Gambit fails and his life is at risk. Yes, he was even willing to kill and get his whole team disqualified if one opponent didn't back off torturing an unconscious Kurama.
After the fights, Yusuke is the one to help Kurama out of the ring. Including at one point, a bridal carry.
At the end of the Sensui Arc after Yusuke has revived with his demon side, he goes to Kurama to get his hair cut back to normal.
It's also when Yusuke gets involved in the demon tournament and meets with Yomi that Kurama switches sides.
There's also the parallels between Yusuke/Kurama and Sensui/Itsuki. Both Sensui and Yusuke end up sparing the respective demon's lives and get everlasting loyalty in return, both Itsuki and Kurama tend to be the schemers to Yusuke/Sensui's sheer power.
If you pay attention, Kurama is actually the one Yusuke is nicest toward while being bad tempered with everyone else and even when he does yell at Kurama, he cuts down on the foul mouth. He also seemed a little too worried with how Kurama was feeling after killing Amanuma.
Not to mention Yusuke is neck-deep in Foe Yay with all of his male enemies at times.
How about Kurama being Foe Yay with Karasu? Major one there.
Even Togashi shipped Karasu and Kurama in his doujinshi Yoshirin de Pon!
Kurama and Kuronue in the movie. It's one of the rare cases of him losing his cool.
And to an extent, Yomi and Kurama. Yomi is very obsessed with getting Kurama back into his fold and getting his support during the demon tournament. He's also the one to help carry Kurama out after the fox demon's last fight.
Let's just settle on "Kurama has a thing with dark-long-haired demons" and leave it at that.
How about Koenma and Ogre, "You'd look a little suspicious carrying a teenage stud in your arms." It is fairly abusive, but still. Also whenever Koenma says "Why don't you ever talk to me like that, Ogre?!" during the dark tournament.
Ho Yay is Togashi's forte. It's very difficult to look at ANY two males' interactions in YuYu Hakusho OR Hunter × Hunter without seeing something there. Yusuke x Kuwabara? Kurama x Hiei? Itsuki x Sensui? Yep. Killua and Gon? Leorio x Kurapika? Even Hisoka x Gon, it's there kids! Tons of Foe Yay in both with the protagonists and some villains? HELLS YEAH.
Either Togashi is really oblivious when it comes to making friendship seem like friendship, the couples are real, or they're just a huge shiptease.