During the ending cutscene, not only have a handful of Wisps managed to rescue Sonic from the black hole, but the normal, non-corrupted Wisps are seen transforming the purple "Frenzy" Wisps back to their original forms.
Yacker's goodbye is also rather touching. He thanks Sonic and Tails for saving the wisps, gives both of them a high five, and leaves with his friends to return to their planet. *Sniff*
A huge heartwarming moment near the end of the Wii version where Sonic shoves Tails into the space elevator back to their world to protect him.
And for the whole scene before that: when the final machine pops up and surprises them, Sonic instinctively steps up and puts his arm in front of Tails in a shielding "get behind me" motion. He doesn't drop his arm at all during the entire scene, even when he and Eggman are exchanging witty banter. It's a small detail, but it's very heartwarming.
This instance in the ending cutscene, which instantly became the iconic representation of Sonic and Tails's never-ending friendship. In other words, their Brofist (which is also the picture for this page, seen above).
For that matter, much of Sonic and Tails' interactions in this game — with all the emphasis on heroics and believing in themselves in their characters taking precedent for so long, it's nice to see a game where even while saving the day the two aren't so intense, palling around and acting like brothers.
Orbot's relief when Cubot's voice finally turns back to normal is somehow touching.
During the final battle, all the wisps you rescue band together to help you defeat Eggman and take back their freedom.
In the DS version, one of the missions has you run into Silver in front of a ride that promises an experience of the future. Silver comments that it's nothing like the future he's from; when Sonic asks what it is like, he says that there are blue skies, and smiling people. "That sounds just like the present." "Heh, exactly." It's a small thing, but after all the crap the kid's been through, that's pretty sweet.