Then comes the school principal, who comes in and laments the waste of potential that Yusuke's life, as it has closed at that point, has come to represent.
It's at that point that Atsuko, Yusuke's mother, breaks her Heroic BSOD and joins in the water works.
Then the kid and his mother come in. Both pray before Yusuke's casket and the kid thanks him. The real jerker comes afterward. The little kid asks his mom if he can play with Yusuke tomorrow, apparently having no grasp yet that he's not coming back (obviously this proves untrue, but no one knows that yet).
And of course, the ENTIRE first half of the episode has been spent showing us what a dick Yusuke was. He did NOTHING to make us care all that much for him up to the point when he saved that kid whatsoever, and yet it STILL manages to tear your heart right out when you realize just how much he meant to those around him. It's tearjerking, but at the same time it's a punch to the gut to anyone who's ever felt like their life had no meaning—a feeling everyone has had once or twice.
However, before he jumped in front of the car to save the kid, Yusuke took the time to make him laugh after almost making him cry, indicating that no, he was not a complete jerk and had his soft side.
The truly heartwrenching part of that scene is Yusuke trying to prevent it, and getting thrown around like a rag doll, pressed into the ground, and given a "The Reason You Suck" Speech for his efforts.
Kurama rushing up to Kuwabara after he is impaled. In the Japanese version, it is very clear that he is crying.
Kurama: "Kuwabara-kun? Kuwabara-kun? Stay with us! Kuwabara...?" (his voice breaks, then he shakes with tears)
And there's the fight against Dr. Ichigaki's team, when Kuwabara attempts to de-brainwash his rivals and only gets bitchslapped to hell and back, but even before he collapses he pleads to them to wake up. Then Yuusuke angrily yells at them... and he sees them cry Tears of Blood, begging him to kill them and free them of their pain.
To elaborate a little, throughout the first half of the fight, Ichigaki's team can only say "Kill!" When Yusuke starts yelling at them, they manage to finish the sentence: "Kill... kill us!"
Don't forget Kuwabara's anguish over Yusuke choosing to die by Sensui's hands, in the hopes that his friends would gain enough power to finish Sensui in his place. All topped off by Yusuke looking at his friends one last time, with a smile, knowing he'd never see them again. He gets better, but even knowing that doesn't stop the tears.
It's not just Kuwabara, Kurama, and Hiei's (especially Hiei's) reactions. Nearly everything contributes to this entire episode being a sobfest. Genkai winds up realizing her pupil's been killed and falls to the ground screaming. And Puu? The adorable little bird-like creature that represents Yusuke's inner self? Since he's an extension of Yusuke, that means Puu winds up dying too, in Keiko's arms. That's right. We haven't just seen Yusuke die, but the adorable little animal mascot as well.
Not to mention that while Yusuke's plan to make them stronger works, the power they gained still isn't enough to beat Sensui. Yeah, they're pissed Yusuke died. Yeah, their power has now reached new heights, but they can't even put a scratch on Sensui and he kicks their assess.
Oh yeah, and at the very end of said episode you have this song playing in the background. As if you didn't have enough reason to cry.
Especially when he tells the others about the utter horrors that he saw in Chapter Black. It's even a tear jerker in-story, as we see the guy horribly break down while speaking, then everyone is stunned and poor Keiko is moved to tears (pictured above!).
Kurama's Shoot the Dog moment with Amanuma (Gamemaster). Kurama was left with only two options, either win the game which will result in the death of a little kid, or intentionally lose and allow Sensui to have his way. There was no Take a Third Option and too much was at stake, so Kurama was forced to intentionally psyche Amanuma out, letting him know that he's going to die if he loses and there's no way out of it. The viewer is then treated 10 heartwrenching minutes of seeing the kid completely breakdown, begging for his life despite knowing full and well that there's no escape. Damn.
The preview for said episode brings it home, as it drops the normally upbeat and exciting music in favor of a somber tune, with Yusuke breaking down at the thought of his teacher dying. Yusuke's last words as the title of the following episode, "The Death of Genkai", really sells it.
Yusuke:"My teacher's walking into a fight she can't win... and nothing is ever going to be the same."
The entire exchange between Genkai and Toguro in the Spirit World after the end of the Dark Tournament, as Toguro walks towards the Gates of Limbo. When he removes his omnipresent shades, the sad weariness in his eyes makes it clear just how much emotional pain he's quietly endured for the last fifty years, and just how tired he was of living.
Genkai: "Don't ever feel regret for the things between us."
Toguro: "No, Genkai, but it would've been a beautiful life."
Puu trying and failing to bring Yusuke some water during his Spirit Wave trial. What makes it so heartwrenching is that Puu is a reflection of Yusuke's spirit, so whatever he was feeling, Puu was too. But he fought through the pain and kept trying to help Yusuke.
The entire mini-arc, to the point were it's just plain painful to watch.