Busou Renkin has many ridiculously sad moments, especially since it gets more emotional each time Kazuki "dies". But the entire episode "No One Can Ever Replace Him" is undoubtedly a Tear Jerker.
Let's go through in order (spoilers ABOUND); he dies in the first episode as the setup, not too emotional as he comes right back—and we don't know him yet. After many battles along with many allies (several of these rather tear jerking on their own), he then finds himself in a battle to the death with his MENTOR! He loses, and tears are shed all around. He survives barely, then goes on a quest to find a way to save himself and stop the big bad. He finds out that he can do ONE or the OTHER but not both. But he finds a third option, which falls apart when the bad guy is just to strong to be powered down by the phlepotonium. He then sacrifices himself by launching both himself and the big bad TO THE MOON! Followed by a full episode of Tear Jerkery.
The above-mentioned battle between Kazuki and Bravo is particularly heart-wrenching, especially considering what preceded it. It was a Beach Episode! Bravo was there hanging out and having fun with Kazuki and his friends knowing full well that at the end of the day, he'd have to kill the kid he'd taken under his wing. During the fight, Kazuki can't bring himself to give it his all when fighting Bravo and is near-fatally wounded, thrown into the ocean, and only saved at the last minute by Tokiko.
Special mention should go to just before Kazuki figures out what his Third Option is going to be. He's just found out that there is a way to nullify the power of Victor-Type beings, but the item in question isn't ready yet, and to make it worse; there's only one of them in existence. He's given the above mentioned choice; use it to stop the rampaging Victor, and save the world, or use it on himself like he originally intended, and not have to worry about hurting anyone in his monster form. To add to the drama, Kazuki's friends and allies all made sacrifices so he could use the cure on himself (his mentor was even hospitalized, possibly even permanently injured), and Kazuki even promised that if he couldn't find a way to stop himself from becoming a monster forever like Victor, he would kill himself; this is the only reason the Alchemist Army stopped trying to kill him. When he goes back to school to see his friends one more time, he winds up on the roof, and contemplates that there really is no choice, as there is only one option he could live with. We're then treated to the saddest, most heartfelt tearjerker of a line in the entire series:
Kazuki: "I'm going to save the world...but who's going to save me?"
Tokiko screaming for Kazuki towards the end of episode 24.