The reveal that the Crippled God was the Narrator All Along, and that the suffering of everyone in the series wasn't for nothing because even if a character died pointlessly their deeds were still recognised.
A friendship of Karsa and Torvald Nom in House of Chains, and this line:
“We have saved each other’s lives, Torvald Nom, and so I am pleased to call you friend, and to think of you as a warrior. Not a Teblor warrior, of course, but a warrior even so.”
Shadowthrone and Cotillion finally showing a little humanity at the end of The Crippled God and reuniting Crokus and Apsalar. Hell, most of the epilogue counts.
Beak's ending. After a childhood of neglect and abuse which culminated in Beak watching his repeatedly sexually assaulted elder brother commit suicide and being unable to save him, Beak, a high mage and soldier in the Malazan 14th, is part of Tavore's invasion into Lether. When the grueling campaign seems doomed to end in death for the Bonehunter marines, Beak sacrifices himself to save his comrades and friends as well as the betrayed Edur, creating a magic barrier comprised of magic from ALL the warrens. Not only does he save every Bonehunter and Edur on the field, Hood personally escorts Beak into his realm where the sweet, innocent Beak is reunited with his brother.