King James of Albion showing that despite being a dick and everything that has happened he still loves his son.
The lingering effects of the mana potion on Karin helping her come out of her shell (for a time at least).
Yui greeting her parents as they disembark from the returning ships.
Asuna sleeping peacefully in a rocking chair, with Yui curled up beside her.
Kirito and Klein just sitting on the porch, drinks in hand, simply sharing idle chatter, laughing at an off-color joke, or just a comfortable silence... Just being a couple guys, no battles, no disasters, just... peace. note Quoted after Retsof; Post #3717, 6th thread.
Kino mentions during the party that Silica suddenly started rising rapidly in levels. Intuition says it's from Kirito's influence. Saying that he did more than save Pina.
Asuna and Suguha's conversation.
More of a Tear Jerker, but the funeral held by Carmella and Kino.
Argo hugging Suisen after the latter's blossoming, and the pixie-turned-mousegirl calling her Nee-chan.
Colbert comforting Enya while watching the debates when Alicia finally mentions The Elephant in the Room.
Montmorency and Guiche chatting before the Royal Gala.
Henrietta's relief upon seeing Sakuya saved from her kidnappers. It goes to show that Henrietta truly considers Sakuya to be a close friend.
Kirito, when asked by Karin about Yui's true nature simply replies, "She is our beloved daughter."
The meeting between the Triumviri (Lord Mortimer, General Gramont and Count laRemee) is interrupted when 400 pixie knights from 20 gardens volunteer for military service in defence of their home. Remember that a typical pixie is less than 6" tall and uses weapons the size of needles, so they will literally be fighting giants.
Eugene and Morgainna talking outside the Kirigaya's home at the start of the third arc. The two of them exchange their real names and commit to at least trying to make a marriage work.