A Song of Ice and Fire/Tear Jerker

Eddard Stark's death and, of course, the Red Wedding. George RR Martin just loves to kill off the nice characters, doesn't he?
Sansa and her snow castle in the last chapter of A Storm of Swords. It really drives home that Sansa is just a thirteen year old girl, who has only ever tried to be what is expected of her and been all but tortured for it. Add to that the fact that she thinks that everyone from her fond childhood memories is dead (and is right in most cases) and you have an extremely touching scene.
- Directly after this scene, although possibly funny in a dark way (Littlefinger thought so, anyways), it's also a bit sad to see Sansa stick the head of Sweetrobin's doll on a stick (like a head on a pike) down in front of her snow castle. Considering she undoubtedly had her father and brother Robb's endings in mind. A pretty dark action to do considering she's only thirteen years old, and goes to show that she's seen some pretty messed up crap in her life.
  - Given that she believed that her younger brother's heads were on spikes above the gates of Winterfell, it makes her version of Winterfell particularly accurate. And horrifying.
- This scene really does drive home that Sansa is a Woobie. She pretty much goes on a happy nostalgia trip and creates a bunch of perfect snowballs, remembering her childhood where she would get into snowball fights with her siblings. After making them, she realizes that she has no one to throw them at and play with. Soon after, Littlefinger comes along, and in a moment where she lowers her guard and tries to play with him by throwing a snowball at him, he instead takes the opportunity to molest and forcefully kiss her, resulting in her almost getting killed by her aunt and being traumatized once again. The poor girl can't get a break and live out her childhood at all.
- Also from Storm, when Jon and Ygritte go down into the cave to make love. "Let's never go back up." Especially when you're rereading, and know what's in store for them.
  - Speaking of which, Ygritte's death in Jon's arms, his only consolation that he wasn't the one who shot the arrow that killed her.
The death of Renly Baratheon made an impact. Not at first-- it is handled very quickly and matter of factly-- but then you realize that his knights and other followers loved him so very much.
- Special mention goes to Loras, who can't even be entirely open, as their relationship was secret.

Sansa: That was when Lord Renly died, wasn't it? How terrible for your poor sister.
Loras: For Margery? [His voice was tight] To be sure.

In response to the Elder Brother's "I am sure he'd rather have a living daughter than a shattered shield" comment:

"I am the only child the gods let him keep. The freakish one, the one not fit to be son or daughter".

Ned's conversation with Arya on her behaviour in A Game of Thrones is already rather sad, with all the foreshadowing of doom. But the little coda, where you learn he has hired someone to teach Arya to actually use her little sword, made me cry. Because it showed not only how much he loved her, but also that - in the whole damned book - he is the only person willing to do something for somebody else, just to make them happy. Without any regards of possible gain.
- Well, him and his bastard son Jon, who gave her the sword in the first place.
All the hell Arya has to go through after her father is executed. That it ultimately takes a toll on her mind makes it even worse.
- One particularly sad scene which exemplifies this is during one of her conversations with the kindly man, wherein he tells her that she's still too much of an individual to be a Faceless Man and he offers her other paths in life. Arya thinks to herself that she has a hole where her heart used to be, and she turns down his other offers because she feels like she's totally lost everything and it's too late.
"They gave his eyes to the crows."
There's a moment in A Game Of Thrones where Robb takes crippled Bran to his room, tucks him in and lets out a small cry as they hold hands in the dark.
- Robb telling Bran that when he's up and about again, the two of them will take a trip up to the wall to visit Jon. Harsher in Hindsight.
Sansa and Catelyn's reactions to Robb, Bran and Rickon dying...
When Daenerys smothers Khal Drogo near the end of A Game of Thrones.
From a preview chapter of A Dance With Dragons. Even Daenerys has trouble keeping her eyes dry:

"What could a eunuch hope to find in a brothel?" she asked.
"Even those who lack a man's parts may still have a man's heart, Your Grace," said Grey Worm. "This one has been told that your servant Stalwart Shield sometimes gave coin to the women of the brothels, to lay with him and hold him."

From A Feast For Crows:

Aemon's blind white eyes came open. "Egg?" he said, as the rain streamed down his cheeks. "Egg, I dreamed that I was old."

- To say nothing of Sam's eulogy for the wise old man when he passes away of old age:

"He was a good man... No. He was a great man. A maester of the Citadel, chained and sworn, and Sworn Brother of the Night's Watch, ever faithful. When he was born they named him for a hero who had died too young, but though he lived a long long time, his own life was no less heroic. No man was wiser, or gentler, or kinder. At the Wall, a dozen lords commander came and went during his years of service, but he was always there to counsel them. He counseled kings as well. He could have been a king himself, but when they offered him the crown he told them they should give it to his younger brother. How many men would do that? He was the blood of the dragon, but now his fire has gone out. He was Aemon Targaryen. And now his watch is ended."

- Aemon cursing and lamenting the fact that he will never meet his grandniece and counsel her. He learned about her existence only shortly before dying.
Jon Connington's chapters have him narrate about how he hopes he can see his home castle before he dies. When he does, he goes to the tower with the best view and takes it all in. Even worse when you remember he's dying of grayscale from saving Tyrion, so he could have easily died without ever getting this moment.
All of Reek's chapters in A Dance with Dragons. What he's been through makes him a mine of Tear Jerkers, but particularly heart-wrenching is when he breaks down in the godswood, wishing only that he could die as Theon.
- The scene where he finally admits what he wanted more than anything was to be a Stark is a particularly wrenching one as well.
- "Sister. See. This time I knew you." Had this troper sweating through his eyes for about five minutes straight. Also doubles as a Crowning Moment of Heartwarming.
- "Theon. Yes. I'm Theon. You have to know your *name*!"
Any time you see Sandor Clegane cry. Especially the first time. And especially the last time. No, wait, especially every time.
Ned's scenes near the end of the first book.
Oberyn's recollections of his sister Elia hit hard, especially one where he recalls her mothering/CutenessProximity toward baby Tyrion, given her horrific death and the equally horrible death of her children.
More quiet than other cases, but Septon Meribald's description of 'broken men' and all the horrors of warfare for the common folk - even those serving in the armies - hits hard, reminding the reader yet again that this is now the reality for so many peasants in Westeros because of the arrogance, pride and ruthlessness of the Five Kings and the lords they commanded. And what makes it worse is that Meribald is still affected by his own experiences and loss of friends and kin, after nearly forty years.
Podrick Payne, at the end of the chapter when he meets Brienne, and at the end of A Feast for Crows. "I was his squire...". The Woobie, more than any other character.
Kevan Lannister's loving recollections of his wife, right before Varys offs him.
When Mandon Moore tries to kill Tyrion and he is saved by Pod. Tyrion immediately thinks that it must have been Jaime, because, in his whole life, only Jaime has ever spared him from anything. Really hits hard how downtrodden the poor man is when the only person in his immediate family he associates with unconditional kindness is an amoral Blood Knight.
Tyrion's final chapter in A Storm of Swords, when the two brothers, who had been closer than almost any other characters in the books, have their falling out when Jaime tells him the truth about Tysha. It's hard to know who to feel more sorry for, but the line "Jaime turned without a word, and walked away," is heart-wrenching.
Kind of a tearjerker in retrospect, but Jon's continual rejection of Stannis Baratheon's offer to make him the Lord of Winterfell because of his vows and because he doesn't want to disinherit Sansa is tough to take in light of Robb's plan to legitimize him as a Stark and make him the heir to the North - which Jon knows nothing about. First you have Jon, still thinking that he's not really a Stark and never knowing that his brother and closest childhood friend was going to recognize him as such. Then you have the fact that Robb was completely right - Jon would, in fact, not doing anything to hurt the 'legitimate' Stark heir.

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