1. The way Spock used to look at him as if he could and would do anything—solve any problem, right any wrong, pull their collective posteriors out of any fire. It's not true; they both learned that through the cold, clear inches of a radiation barrier, still Jim misses the way it used to feel to have Spock look up to him that way.
Maybe Jim isn't being entirely fair. It could be that Spock still does look at him like that, but the keenness of the patent lie strips all the joy from it.
2. That ragged scar from the flintlock blast. It sounds so silly to miss a scar, but every time Kirk looks down to run hand or tongue over the unmarred expanse where that terrible proof of their history used to lie, he is reminded afresh that despite whatever occurred on Seleya, in some existential way that he will never understand, this is not The Spock he has always known.
3. That exquisite little patch between jaw and neck which—when stimulated—used to leave Spock helpless victim to sensation. The first time Jim found it was the first time he saw Spock laugh out loud. Then the laughter gave way to a frantic sound—back then utterly alien, but now as familiar to Jim as his own heartbeat is.
After Genesis, that spot was nothing special: only skin.
4. As they meld, never being sure which memories are real and which have been artificially enhanced by the healers. If he can't tell, it doesn't matter, Kirk lies to himself as his body cools, but it's the first time in his entire life that he's been unsure of Spock. Only in this loss does he realize what it was that he had.
5. More than anything, Jim misses the mistaken belief he used to hold that James T. Kirk could pull though anything if he set his mind to it. He misses the brashness of the man he used to be before he understood just how much pain a loss could bring. Jim has to face fear now where he never has before, because then he simply didn't realize what lay at risk, and now he does. For all his intellect, worldliness, and experience, Jim hadn't the slightest idea what genuine grief was like, and he much preferred things that way.
But it does make all the other losses seem inconsequential, so Jim wraps his arms around Spock and pulls him more tightly against his chest.