Twilight Sparkle spends most of the story being completely terrified of Dusk Shine, partially because she isn't sure how she should relate to him. When she finally goes to meet with him and realizes that he's like the brother she never had (keep in mind this was written before anyone knew about Shining Armor), just about all of their interactions from that point on become instant "D'AAAAWWWWW!" moments.
Fluttershy and Butterscotch. They're adorable enough on their own, but when they encounter one another...
Philsterman10 did a collaborative voice acting of that scene which can be heard here Just try to pick up your fragmented heart pieces on your way out.
Elusive and Rarity's final exchange in which he urges her to choose Sweetie Belle over him. It goes a long way to showing that Elusive is every bit the Element of Generosity that Rarity is.