Sweetie Belle after the race in "Neigh, Soul Sister". "Set phasers to HUG!"
Also Rarity putting off the Coming of Smooze for a year so she can save her sister's soul in the meantime.
Then there's the following exchange:
Rarity: Oh no! Now who shall hug me? [beat] Sweetie Bot:Sweetie Belle!
While it's played for laughs, "Sweetie's Big Race" is pretty heartwarming, as the lyrics coupled with their delivery (even in a robot monotone) really show that Sweetie Bot is having fun in the race.
"Running in a circle yes! Having lots of fun hooray!" "I am running oh so fast! Fun levels are to the max!"
For as much as it's bastardized, the interaction between Applejack and Applebloom in "Neigh, Soul Sister" is still pretty heartwarming by this show's standards.
Pinkie's parents being resurrected by the portals. Granted, they're babies, but she's not complaining. Especially when there is a brief reprise of the last line of "Pinkie's Brew" seeing as how now that rather depressing line has been resolved.
Pipsqueak cheering up Luna is just as nice in the show as it is in this show.
"We don't care if you won 50 iPod nanos, you're the best Apple thing of all."
The fact that Applejack was trying to keep her friends away from the bomb. Why? Because she wanted to protect them. There is absolutely no ulterior motive here. When you consider the fact that the show runs on Comedic Sociopathy, this is pretty heartwarming. The episode is pretty much proof that Applejack is the third-sanest pony in the show, behind Pinkie Pie and Cadence. Well, she is the element of LoyaltyHonesty.
The background ponies' quips are usually funny, but in "Cherry Bomb" one of them can be heard shouting "Applejack is my hero!"
At least in the crapsaccharine world of FiW, the idea of ghosts whose only purpose is to give fillies free milkshakes and movies is very sweet.
The last thing Rainbow Dash says to Twilight before the latter goes into the portal in Horse Women?