Anytime he tells his fans how awesome and encouraging they are.
*Description of YouTube channel* "I've been making Let's Plays here for over 3 years now, and really appreciate the support from every one of you, not to mention the many of you I've actually met at conventions this year!"
In Majora's Mask, at the end of the Anju and Kafei sidequest, during the final scene where the two exchange their masks, Chugga stays completely silent throughout the whole scene, not even reading the text like he normally does. Then, afterwards:
Reminising about two Gabby and Ty cosplayers at an official Nintendo event that he befriended.
Chugga said in his Pokémon Crystal LP that Wooper is awesome because, "If you can look that happy all the time, and have no arms, you are amazing, and you are truly a king among kings." That's not the heartwarming part. A user by the name of Kawaii Baka Daysu left this comment:
Kawaii Baka Daysu: I was watching this episode with my cousin who was born without arms. When you said that true fact about Wooper, my cousin burst out laughing saying "THAT'S SO TRUE!!!" Thank you for making my cousin laugh.
In one of his bonus episodes for Emerald, he rants about how he had to spend over $140 just to get all the materials needed to show the battle for Latias. The very fact that he went through what he described as "hell" but did it because he loves doing these videos is very sweet.
His four-year anniversary video, in which he not only thanks all of his viewers, but also brings up how a small, ten-second comment of his from a Luigi's Mansion episode about how he could never stick to exercising led to users sending him loads of encouragement and tips, which actually allowed him to finally stick to a routine.
He also mentions how let's playing has helped him become less shy, which is also pretty sweet.
His rant on Peach's dream of being surrounded by miniature Marios and his rather symbolic rant on what it represents. It was a parody of this trope, but could be considered an example all the same.
After encountering a Cragnon in Super Paper Mario complaining about his camera job, Emile gives us this:
"Maybe they just don't understand the value of videos. Maybe they don't understand how many people you make smile all over the world for making videos, and that is exactly why making videos is the best thing in the world."
In Okamiden, Chugga says he greatly respects everyone who edits his TV Tropes pages on a regular basis.
This tweet... if you needed any more proof that Chugga and Jon are good friends and their rivalry in TRG is friendly... look no further.
Constantly gushing about how much he loves the music of Jolly Roger Bay (and the level as a whole by extension) in Super Mario 64 DS.
A more general example from the same LP: because for years Chugga has defended Super Mario Sunshine, calling it underrated and superior to Super Mario 64, and said that he would never LPSuper Mario 64, the idea has grown up that Chugga doesn't like 64. In this LP we see that this is untrue, he loves the game and has great childhood memories of it, he just thinks Sunshine is even better.
This becomes even more heartwarming when you realize that Stephen and Mal only make logos for him, LOGOS! He gave him all that, just because of the logos they made him.
He provided Stephen and Mal with such amazing gifts not only because they make logos for him, but because they are such great friends. Stephen and Mal offer him to stay over and hang out fairly often (as made evident through Emile's various appearances in Stephen's vlogs) and THAT (the friendship they share) is what makes it truly heartwarming.
During Geek Week on Youtube, he and many of his fellow members of Polaris talk about how Video Games have had a big impact on their lives. he openly states that "Super Mario 64" and Pokemon Red and Blue are games that he owes everything.
When Chuggaa was outed as a brony, some people decided to be assholes, but majority of his fanbase didn't have a problem with it.
This got better. A member of a fangroup for chugga on deviantART posted a journal for the group about how him being a brony isn't as bad as some thought.