The Wisps return, including Yacker◊! The Wisps are back to help Sonic even though they don't need help back. It brings a smile to your face.
Made better by the fact that they don't even factor into the story. They simply show up to be of use if Sonic needs them.
The way animals come out of robots you destroy and containers you find can be this in a somewhat nostalgic sort of way. The first trailer particularly has Sonic showing up in his usual Big Damn Heroes way to save a group of them from The Deadly Six, who all huddle together behind him.
In the opening cutscene, Sonic clearly cares about the animals Eggman has abducted. A LOT. Unfortunately for him, Eggman is able to use thisto his advantage in order to distract Sonic and Tails so he can shoot the Tornado down.
After Frozen Factory Act 4, when Eggman saves Tails's life from a rogue Cubot.
Similarly, when Eggman saves Sonic's life at the beginning of Lava Mountain. He may have ulterior motives for keeping his foes alive, but it seems as though he has some fondness and genuine concern for his enemies. He's a complicated guy.
Upon beating Sky Road Act 1, we get treated to a cutscene where Orbot requests to be Sonic's new sidekick should they fail to rescue Tails. Even though Sonic rejects his offer, Orbot does show some admiration for Sonic's determination, and notes that Tails is lucky to have a friend like him.
Just before Lava Mountain, Act 3, Sonic finally meets again with Tails, who's now looking completely robotified and under the Deadly Six's control. But, as Zavok orders him to shoot, Tails blinks at Sonic, revealing he's not a robot slave at all, and shoots at the Zetis (while shouting a Big "NEVER!" in response to Zavok), forcing them to retreat. After all the pain he suffered throughout the game, it's a big sigh of relief to see Sonic reunited with his best friend and finally smiling and ready to kick butts again.
Sonic: "Good to have you back, Tails!" (cue Brofist)
After the final boss, there's this exchange between Sonic and Tails as the fox is reprogramming Eggman's Extractor to bring their planet back to life. Quick, simple, maybe not entirely satisfying considering their falling out in Frozen Factory, but still cute in his own way.
Tails: "You know you never needed Eggman, right? I could have turned this off myself."
Sonic: "Sorry about that, Tails. I'll never doubt you again."
Tails: (smiling) "It's cool."
In the ending before the credits start rolling, Sonic just lies on the green grass, closes his eyes, and takes a deep breath to enjoy the air of his beloved planet before falling asleep. As the screen goes white, we're able to see Tails, Knuckles and Amy about to join Sonic in his rest.