When Tom risked his prized Maxxor card in the "Castle Bodhran or Bust" two-parter in order to save Reggie, somebody he barely knows.
Bruiser, the kid who beat Tom hands over his Castle Bodhran scan once he learns what the stakes really are. (Although it's not as generous as it sounds since before the match, he went back to Castle Bodhran and scanned it again so that even if he lost, he would still have a backup scan.)
Bruiser: Castle Bodhran, compliments of the Bruiser. I used to be a nice guy too.
Also, Tom's reaction to meeting Maxxor for the first time. Despite it turning bitter-sweet when Maxxor acted like a jerk. At least for part one anyway.
When Maxxor healed Kaz in "Castle Bodhran or Bust Part Two".
Maxxor: Tom, you and Kaz have more than proven yourselves. Now I'll return the favor.
After Kaz accidentally gets Blugon caught in an energy field during a scanquest in "Out In The Cold". He tries to deliver the mugic Bulgon was going to give to his friend Raimusa in Blugon's place. After a long trek he finally arrives at Raimusa's just as Pyrithion's attacking. He gets the mugic to Ramiusa, who uses it to defeat Pyrithion. After the battle Raimusa considers Kaz a friend.
Ramiusa: What is your name?
Kaz: You can call me Kaz.
Ramiusa: I will also call you, friend.
Siado once tried Taking the Bullet for Prince Mudeenu in "A Flux Too Far", he lived of course. Still, it was nice to see the normally snobbish Mudeenu care about one of his men.
Mudeenu: Siado!
Siado: Just doing my duty.. Sire...
Maybe minor, but in the episode, "Maze of Menace", when Tom was being chased by Chaor, Tom shouted for Maxxor's name. This was when Maxxor is deathly scared of everything and knows that he can permanently lose his powers at any given moment. He still comes to Tom's aid. That's a true friend for you.
After Maxxor had his courage restored to him he got into a Group Hug with Intress and Najarin.
The fact that his immediate reaction when Chaor takes a cheap shot at Tom is to block it. It's in that moment, and when Maxxor saves Tom from that cave in, which is also heartwarming, that you realize that Maxxor really has accepted Tom as an ally, and is just as protective of him as he would be for any other Overworlder.
Peyton and H'earring in "The Codemaster Chronicles Pt 1", when Peyton went out of his way to save H'earring in the Lava Pound.
When H'earring tried telling Tom to save himself. It's nice to see that he actually care's about Kaz and his friends.
The gang met and made friends with Iparu in the episode "The Ultimate Scan". Iparu is a pretty heatwarming guy.
When Peyton tore up his map of Iparu's home.
A good portion of "Dangers of Diplomacy" was pretty heartwarming when you think about it. It's the first time we really see Maxxor relax, not having to worry about his or his tribe's safety for once. He even tells Tom and Kaz a story from his childhood, which is a stark contrast to how he treated them before.
The story Maxxor tells Tom and Kaz about how he and Raznus first became real friends was pretty heartwarming in itself.
Sort of a case of fridge heartwarming, but when Chaor was attacking the Arsenal, Tangath-Toborn tosses up his signature battlegear, the Sword of Khy'at, to Maxxor to fight against Nalfarr. You find out later that the Sword of Khy'at is essentially Tangath-Toborn's lifeline, if it was somehow destroyed than he would have become a spirit and have been forced to leave Perim forever. And he didn't hesitate for a second to give it to Maxxor to help. Like brothers indeed.
Conner telling Peyton how to find a conjurer in "War Beasts", after working with Klay and Krystella to scam him. Proves that unlike the other two, he isn't a total douchebag.
Fivarth revealing his identity as a conjurer to Peyton and Kaz once he's told them of the conjurer's origins.
Peyton: (thoughtfully) So the Mipedians owe the conjurers, everything.
Peyton giving Sarah a Bear Hug and calling her "Sarbear" in "Warriors of Eternity". Upon finding her alive and well after days of searching for her.
Tom finally stepping up and telling the school shrink that Perim is a real place in "Earth to Kaz" in order to prevent Kaz from being labeled crazy.
In the season 1 finale, Tom is shown to have a scan of Intress. This might seem odd, given that very few characters are shown to play as Intress in the battle drome (Intress is one of the few creatures who has a vast majority of appearances in Perim), so she is obviously rare. However, given all that Tom has done for the Overworld, such as saving Maxxor's life and ensuring that the mugics of Perim remain working, and is evidently shown to care about the Overworld's safety, it wouldn't be too much of a stretch to see Intress allowing Tom to scan her out of respect for all that he has done.
A rather nice blink-and-you'll miss moment happened in "Underworld Overthrown". After Takinom and Rarran are given the signal to retreat (so Chaor can fire the Annihilizer) Rarran hesitates and asks about the still mind-controlled Underworlds still in harm's way. Takinom tells him they can't save them, and she orders him to retreat. Instead, Rarran flies back and throws some kind of attack, then quickly catches up with her. After Chaor fires the Annihilizer, it turns out the mind controlled Underworlders survived. All thanks to Rarran hitting them all with a "Flame Repel Attack" just before the blast hit. Just goes to show the Underworlders aren't all Chaotic Evil after all. Turns out to be a tearjerker when it's quickly discovered he got hit by a M’arrillian Mind Control attack and is now their puppet.
During his match with Code Master Hotekk in "Hotekk's Challenge", Tom reveals that Dardemus. While a scary looking Underworlder, is actually a Bruiser with a Soft Center who became friends with Owis during the war with the M'arrillians, and Dardemus was now teaching Owis to do fire attacks.
Tom also revealed that Vidav had for some time been using Mugic to help restore Hoton to health.
It's small, but the scene in "Elementary" when Peyton humbly asks for a scan of the elemental of wind. After briefly consulting Enre-Hep she grants his request in a very pleasant manner (way different from their first encounter).
Silv: Do as you wish friend.
It goes even further when it's revealed that Peyton befriended a M'ARILLIAN. Proving that despite the tribe attempting to flood Perim? They too have good creatures amongst their tribe.
The end of "Stelgar Strikes", Stelgar is a creation of Mommark and is a tiny starfish like creature who becomes bigger and much more dangerous when exposed to sunlight. At the end it is driven off and is shown to have shrunk back into its original size and is sucked into a whirlpool believed destroyed but is seen drifting through The Underworld, it opens its eyes and is spotted by Rothar a large Minotaur like creature who upon seeing him helps him up out of the water.
Heck, the fact that any of the creatures that were known to have been created by the Overworlder Mommark, at least after the M'arrilian Invasion, are still accepted and treated as other Underworlders by Underworlders, especially due to some of the other creations causing them lots of trouble, like when Staluk nearly killed Borth and Majar.
The ending scene of "Tale of Two Toms", where Tom's friends ultimately choose him over CoolTom, saying they prefer the "classic non-cool Tom" over the jerkish cool version. They even have a friendly chat where they say he's "kinda cool" compared to Kaz.
During the flashback in "World's Apart", when Aivenna spies Nivenna apparently being attacked by Takinom (not knowing that they're just sparring). She rushes in to help and attacks Takinom, even though she barely knows her long lost sister.
Maxxor, despite being fully aware that Kaz idolizes Chaor, his archenemy, and has even been seen with him, clearly still sees Kaz as a friend. The same could go for Chaor as well, as despite his harsh upfront form with Kaz, occasionally threatening him, Chaor clearly has a soft spot for the human, despite being aware of his friendship with the Overworlders.
The episode "Blight Flight" showcases that Tom has spent a long-time exploring ways to try to get rid of the sentient blob monster at Prexxor Chasm. He goes through great lengths and puts his life on the line multiple times only because it's the right thing to do, only made more heartwarming when Smildon rather fails at being subtle in regard to how grateful he is to Tom for his efforts and how much he's come to care for the human. After the disease is destroyed, Tom's relief and happiness over seeing that Smildon survived is met with Smildon finally dropping his tough exterior attitude and loosening up with his new friend.
Najarin finally allowing Tom to scan him at the end of "Eye of the Malestrom". Solidifying that the boy has proven his worth to the Muge after everything he has done, and now considers him not only trustworthy enough to not abuse his knowledge, but as a friend.
In "Going Under", Kaz tries to instill an appreciation for Underworlders in Tom by coaching him while he learns to play with an Underworlder deck. Tom eventually becomes so good at it that he starts getting hailed as an even better Underworld player than Kaz, much to the latter's irritation. However, at the end of the episode, Tom reveals to Kaz that he only got so good by studying the footage of Kaz's previous matches, because he knew he had to learn from the best.
Chaotic Evil after all. Turns out to be a tearjerker when it's quickly discovered he got hit by a M’arrillian Mind Control attack and is now their puppet.