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 drops 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.