This can be extended further, given that more than one of the tournament guests have cited NCS as their main inspiration.
If something that looks serious happens to one of the guys, the others will sound genuinely worried about them, even Jon.
The guys recorded Super Smash Bros. Brawl at Jon's house and LittleBigPlanet at Chugga's house. Jon is Canadian, which leaves a good distance between the Wisconsin-based NCS and a massive distance from the Floridian-based Chugga. The guys are officially close enough friends in real life to traverse the country just to hang out.
On one of Tim's BreakingNCS videos, a comment war suddenly started up about whether Chuggaaconroy or Nintendo Capri Sun was the better Let's Player. After the fight started to go too far, Jon left this comment on the video:
Proton Jon: Guys, both Tim and Emile have gone through a lot of shit in their lives, and both have found success and enjoyment in LPing. I understand not liking someone's LP's or thinking one person's a better LPer, that's having an opinion, but saying you hate the actual person when you've never met themselves seems kind of ridiculous, don't you think? All you see through LP's is a filtered version of a person, you don't know everything about them.
Jon made a Formspring post in response to people questioning his apparent rivalry with Chugga. For those who don't want to read the whole thing, it basically says that Jon actually does consider Chugga good friend, and at one point at Magfest, the former got very sick and Chugga stuck around to help him get better, checking up on him and keeping him company. The final line sums it up amazingly well:
Proton Jon: No matter how stupid our bickering back and forth might be in videos, know that I legitimately like the guy and consider him a very good friend, and watch over him like an older brother would.
The fact that Chugga and Proton Jon treat Tim kindly, even though they're supposed to be competitive.
Not on the TRG channel, but during part of his own play through of Mario Party 2, NCS selects Mario and DK as two of the NPCs and— fairly consistently— refers to them as Chuggaaconroy and Proton Jon.
NCS: They're not really here or anything, it's just... I don't know. I guess I miss them and so I decided to invite them in somehow.
After the Thrown Controllers event, the guys personally invite Diabetus to play Battletoads with them to make up for leaving him out of the Battletoads event in the panel.
When Jon tells the story of how they met one of Chugga's fans before even arriving at Magfest, then saying how awesome it was that they met her.
During Bowser's Magma Mountain, when Jon lands a Chance Time that causes the CPU to give all of its stars to Chuggaaconroy, resulting in him winning the game, Chugga's response is to literally hug him.
At one point on Peach's Birthday Cake, NCS describes his time at the convention with the other Guys as "These have been, like, the best three days of my life. I'm not even kidding."
Throughout the series - mainly after the first world or two - Jon is constantly trying to kill Chugga. That's not the heartwarming part. The reason behind this is because Chugga ended up nearly giving him a black eye with a pillow (it was one of those cylindrical pillows stuffed with hard foam, so it hurts a lot) and he's just venting anger. He brought this up in an interview, and stated Chugga's actually a really great guy, and now that he's gotten over the incident he's ready to move on. In the interview he also says Tim is one of the nicest people he's ever met and that he'd really like for Josh to come back and guest star in another LP later on. It does make up a bit for the massive trolling he's been doing lately.
Maybe even gets more heartwarming when Jon says Josh is like a younger brother to him.
During the end cutscene, the Guys' commentary as if they're actually the characters onscreen (Chugga is Mario, NCS is Luigi, etc.) is a bit heartwarming. Knowing them, they'd normally have some satirical and sarcastic jabs at the scene. (Except maybe for Tim.)
In Episode 7 of NSMB Wii, the guys go to collect the third Star Coin in World 4-3. After they enter the room where it's located and see that the Coin is encircled by many other coins in the shape of a heart, the guys give a collective "Aaaaawwww..."
In Episode 9, Jon and Chugga agree they should probably let Josh and Tim get more lives. Probably. They do end up giving them the first shots in the 1UP minigames from then on.
In Episode 4, when Link and Yoshi first appear, Chugga and Jon are the ones playing, meaning Tim isn't able to be the first one to play as Yoshi. When Chugga mentions this, Jon kindly sacrifices his turn and gives the controller to Tim so he can play.
Somewhat heartwarming was a few seconds later, Chugga remarks how "nobody can hurt Tim when he's so happy". Tim then receives damage almost instantly. Chugga's response to this, though likely supposed to be funny, is actually pretty heartwarming too:
Chugga: How dare you hurt him when he's so happy! I will decimate you for that! *kills enemy*
Episode 6 opens with a painful-sounding thumping as Chugga takes a tumble. The other two immediately check on him and are obviously worried, even as he decides to Throw It In.
In episode 13, Chugga is confused about the "Canadian flowers" and making fun of them. Turns out the flowers he's referring to are poppies, and when he learns about the whole "Remembrance Day" reason behind them, he outright states that he feels bad for mocking them.
From the final (story) episode, Chugga and Tim fight the final boss. After getting a Game Over, Tim decides to let Jon have a go at the fight, saying they should continuing rotating. This allowed all three to get a chance at the final fight, with the added bonus of Chugga and Jon working together to finish off the last enemy in the game. It also allowed all three of them to end up with the same turn count, both total and for the episode.
Bowser Land. First turn, NCS gets a hidden block with a star in it. Chugga delivers this line:
Chugga: I think the game just realized that Tim's not playing bad, he deserves to win something.
Near the end of Bowser Land, Jon is debating on whether to steal a star from NCS or Chugga*
NS has 2 stars, Chugga has one, and Jon has a Magic Lamp and was on his way to get a star in the first place.
After teasing the two, and the viewers, on his decision he's about to go for Tim...but changes at the last minute and steals Chugga's star.
However, this may have been part of his plan, as in the end he ended up winning the board because he stole that star; if he stole from Tim, Chugga would have won due to getting enough Bonus Stars and having more coins than Jon.
Jon was glad he won the project, no shocker, but since he stated that he grew up with it, you just had to smile a bit during that statement.
Mixed with CMoF, Chugga being happy to fail so many times in mini-game roller coaster with Wario just to send "D'oh, I missed!" off with a bang, since it doesn't appear in Mario Party 3.
During the Minigame Coaster, the guys frequently help each other out, such as Chugga and Tim helping Jon remember the button patterns in Move to the Music.
At the start of episode 7, Chugga starts out lamenting that this is the last night they have together, he then gives Tim a White Yoshi to help him further his collection and gives Jon a poison mushroom that actually looks like a poison mushroom this time (the last one was apparently a mini shroom, and Chugga just lied to the internet about being a poison one). He ends it off by letting Tim do the intro.
In episode 9, Jon brought up the fact that, because he tends dislike people bringing up the old memes that people think he's actually a jerk who overreacts to such instances, bringing up that in these cases he's actually laughing about it and isn't as annoyed by it as the LPs tend to let on.
The Guys help each other out on the challenge rooms. They even cheer on the person currently playing as Kirby and Emile gives Tim a good luck hug before his Sword run. He also attempts to pat Jon on the back after apologizing for making fun of his Wing run, but it looks like he's hugging Tim again from Jon's point of view.
On the Yoshi's Island board, Chugga putting everything he had into supporting Tim at the end, even when Jon looked like he was going to win. This includes giving all of his money to Tim and actively avoiding Jon's properties. Tim wins.
The comments on this Let's Play so far have been pretty vicious, with people insulting Tim's playing ability and being disgusting towards Lucahjin due to her gender. The Guys' comments to some of these have been heartwarming as they stick up for each other and put the trolls in their place.
Chugga gave even more presents to the friends on the Runaway Guys. Tim got a Pink Yoshi, Jon got a "Batman for President" t-shirt and Lucahjin was given a Barbie and Mah Baaaalls.