It's made worse in that David saw his life's work fail right before his eyes, and he ends up being blown up with it.
Even worse; he died knowing that his life's work had failed because of him. His arrogance and pride lead to the deaths of the other researchers on the Genesis project, Khan and his followers, and the crew of the U.S.S. Grissom, and it was all for nothing.
Want to know what makes it worse? (if that's possible) Word of God says that the genesis effect would have worked fine had the procedure actually occurred on a planet like it was intended.
As if all the above isn't enough, pay attention to the rest of the Enterprise crew as they react to Kirk's heartbreak; notable are closeups of McCoy - Kirk's best friend next to Spock himself - and Scotty - who lost his nephew in the previous movie.
The destruction of the Enterprise, which is truly the death of a character in and of itself. This is the ship which saved Kirk and crew (not to mention the whole galaxy) so many times in TOS, and now they're forced to sacrifice her to save Spock.
The visual effects company ILM was more than happy to blow up the model, which was oversized and unwieldy for the team.
Bones' scene with Spock in sickbay, showing that he really does consider Spock a friend/brother.
"I'm gonna tell you something that I never thought I'd hear myself say. But it seems I've...missed you. I don't know if I could stand to lose you again."
Perhaps a bit unusually, KRUGE gets something of a Tear Jerker scene after the destruction of the Enterprise takes the lives of apparently his entire crew save Maltz. The very next scene we see Kruge in, he's hunched over in his command chair on an otherwise-empty bridge, head in his hands, grieving very visibly for the loss of his men. The moment passes quickly, but still.
He also had a moment when his pet was electrocuted during the volley from the Enterprise.
"Forgive me, T'Lar. My logic is...uncertain, where my son is concerned." To hear the pinnacle of Vulcan control wrestle with his emotions, and admit that he cares more for his son than for doing the logical thing, it brings a tear to the eye.
"To absent friends." Especially when you consider that a fair number of the Enterprise crew were seen during Saavik's Kobyashi Maru test, meaning that they were a part of the training cadre, much like how Scotty was in charge of the Engineering cadets. To them, the crew weren't just a bunch of trainees; these were men and women that the senior officers had been teaching and getting to know, and they had just watched them get slaughtered during Khan's rampage.
Yes, Esteban was a bit of a "Rules Nazi", but it still brings a tear to the eye to think that him and his crew, a bunch of scientists on the almost defenseless U.S.S. Grissom, were gunned down before they could even react.
When the scarred Enterprise pulled into spacedock, with a saddened Rand watching on.
Kirk reliving Spock's death when Sarek mind-melds with him. His whispers of "Spock..." and "no" are absolutely heartbreaking.
Spock's resurrection and the overjoyed crew.
"USS Enterprise, Captain's personal log. With most of our battle damage repaired, we're almost home. Yet I feel uneasy, and I wonder why. Perhaps it's the emptiness of this vessel. Most of our trainee crew have been reassigned. Lieutenant Saavik and my son, David, are exploring the Genesis planet which he helped create. And Enterprise feels like a house with all the children gone. No, more empty even than that. The death of Spock is like an open wound. It seems I have left the noblest part of myself back there...on that newborn planet."