Chris Thorndyke may have annoyed the living heck out of 80% of the viewing audience but anyone can well up watching the end of the second series of Sonic X, when Sonic takes him running one last time, before he has to do the whole return to his own world forever thing. It's summed up in the fact that Sonic cries for the first time pretty much ever in that continuity, and the kid gets the tears in his face. That you never see Sonic's eyes just makes it worse.
Similarly, in Sonic X, Cream's reunion with her mother.
Sonic X again. During the episode Last Resort, Amy makes Sonic a bracelet out of shells to protect him when he's around his weakness, water. Instead of being all put out the way he usually is when Amy makes a romantic gesture, Sonic can only stare at her in surprise. The look on his face, coupled with the look on Amy's, is absolutely adorable.
Add this to the fact that after the bracelet is smashed , and Amy is convinced it's lost, the episode ends on a scene with Sonic, watching the water and wearing the repaired bracelet. Awww.
The ending to Episode 52, Memories of the Wind. There Amy has waited for a good while for Sonic to return. When he does, Amy rushes to him, yells at him while in tears, then finally declares she would have waited for his fateful return for the rest of her life. THEN she screams for Sonic to just tell her he loves her. Sonic responds by giving her a flower and an answer...which is inaudible and thus ambigious. But it works so well that you're likely to be "awww"ing throughout.
Made even better by the fact, in the French Dub, Sonic ACTUALLY says he does love Amy!
Near the end of the final season the crew will have to use the Master Emerald against the Metarex. The fate of the universe is on the line and it's literally their last chance... and Eggman points out to Chris that if the Master Emerald explodes, he's going to lose his only chance to go home. He's no doubt expecting an immature response much like the one he would've gotten from Chris when he was twelve years old... except Chris doesn't answer, he just turns around and goes back to work. Because it's the fate of the universe at stake and that's no contest. Still you can see how much it tears him apart, and it takes on a new significance when you remember that Chris, the boy who once risked destroying all of time just because he didn't want to let go of Sonic. Now he actually wants to leave Sonic and knows what he's giving up if he stays... and he still gives it up, just like that. Took him sixty plus episodes but he got there in the end.
Sonic giving Amy a rose in the final episode of the second season.
Tails and Cosmo's goodbye kiss is both this, and a Tear Jerker.
Chuck hugging Tails goodbye at the end of the first season was almost as emotional.
Tikal arriving to take Chaos home in the episode "Flood Fight".
It's kind of surprising that Chris gets a few of these, considering general fan opinion of his status in the show. The 0.9 percent of the time when he's not being a pain in the ass are actually rather sweet.
If you want to be specific, there's a moment in an episode near the end of the final series when Chris chooses to forgo his chances of getting home so that they can use the power of the Master Emerald to save Sonic. Half the audience was probably thinking the same thing as the robots were: "God damn, the kid's finally grown up." It makes the point where he actually does go home even more heartwarming than it already was.
Sonic and Chris's final goodbye at the end of the series. The dub's Sonic jingle that plays in the background added something majestic to the scene. Doubles as a Moment Of Awesome.
And for bonus points, Hironobu Kageyama is one of the singers of the Japanese opening. How appropriate...
Sonic befriending Helen and blithely refusing an invite to a big public event involving the President to take Helen to an island is a doozy of Heartwarming. Determined to bring Sonic to the event, one of the government officials goes as far as to send helicopters and guards to force Sonic to go to the event. Of course, Sonic manages to bring Helen to the island and it looks as if she is going to cry with fear. However, she burst out laughing because she never had so much fun in her life. Then by the end of the episode, Helen's overprotective parents realizes Helen's joy in adventure and decide to spend more time with her outside.
ESPECIALLY episode 38, in which Live & Learn plays through the scene of Sonic & Shadow using Chaos Control. In the Japanese and French versions, anyway...
Unfortunately, the 4Kids dub does away with most of this, and plays the same music for almost every situation, ruining some of the more emotional scenes.
Amy's bond with E-102 Gamma in the Sonic Adventure adaption. It was cute in the game itself, with the anime's refined animation and dialogue however it's upped a fair bit. Perhaps most notably Amy defending him after his battle with Sonic, the guy's probably never had someone care for him, let alone on the verge of tears about him.
The comic book adaption, Eggman poses as a wrestler (El Gran Gordo) to help make profit for his machinery, it is quickly revealed however that the doctor has become accustomed to his new alter ego, and enjoys being popular for once. After a suspicious Sonic challenges the doctor in his wrestling alias, he finally overpowers him and gets ready to take off his mask and reveal him. However the doctor quietly begs him to let him keep his new identity and be loved for once in his life. Sonic is hesitant, but complies, and "El Gran Gordo" graciously congratulates the victor of the match.
The television series focuses a lot on the relationships between the characters. Not even Eggman is exempt from this, as his hench-bots - specifically Docoe, Bocoe, and Bokkun - gradually come out of the background and become full-fledged characters, complete with a few mini-arcs. While each have their own quirks, the three together with Eggman ultimately come off as a sometimes-dysfunctional family.
Particularly memorable is when Bocoe and Docoe strike out on their own for a while, and Eggman tries to cook Bokkun a meal and fails miserably. That, and Eggman takes them back without a second thought, something that Sega's wrathful Eggman would be hard-pressed to do and that Archie's machiavellian Eggman would never consider.