The first time it happens, it's after he returns. He understands the anger, why John was violent towards him, (faking his death and everything, so sorry about that by the way,) but he doesn't understand the tears.
"I thought you'd be happy that I came back," he says, confused.
"I am you idiot," John mumbles.
Sherlock frowns. Then what was it? "Did I say something wrong? Are you angry?"
"No... no... it's good. These are happy tears."
Sherlock ponders that. Happy tears. Who would have thought?
It happens again at the wedding, and at first, Sherlock is concerned that he said something wrong, did the speech wrong, because weddings were supposed to be happy, and did he do something wrong?
But John tells him it was perfect and hugs him and Sherlock realizes they're happy tears.
When John and Mary are on their sex holiday/honeymoon, Sherlock nearly relapses. Drugs are so easy and he's so bored, and it really wouldn't be any trouble at all to just slip the needle into his arm...
Instead he texts Lestrade, and the man shows up in record time to talk Sherlock down and clean the flat.
He stays with him for the next couple of days, and when they finally talk about it, Lestrade is so proud of him for not giving in, that he cries a little bit.
(Then Sherlock goes and throws that away, but it was for a case, okay?)
He's in hospital (the second time) recovering from his gunshot wound when Anderson visits him. He's surprised, because... Anderson.
But the man is considerate and manages to not be annoying, so Sherlock is civil. He even tells Anderson that he was there, in his mind palace, helping him, and the man is moved to tears.
He hugs Sherlock, and it hurts, but Sherlock allows it, because he's been told that happy tears are good things.
Mary is eight months pregnant and miserable when Sherlock drags John on the case. He sets up shifts of friends and neighbours to take care of her, and drags John off to the Harry Potter Tour. He doesn't tell John where they're going, only that there's a case.
(There is, sort of. Okay, maybe not.)
When John realizes what Sherlock set up for him, a break, to one of the places he'd most wanted to go (see, Sherlock did listen) before the baby came, he threw his arms around Sherlock, and there was definitely sniffling.
John adamantly denied it, of course.
The last time it's his eyes that fill with tears when John asks him.
"Would you be the godfather to our baby?"
Sherlock looks down at the bundle in his arms, and suddenly can't see her for the tears.
If Sherlock could see, he'd know that John was crying too.