The scene at the beginning of the episode where Gwen and Kevin say goodbye to Ben before leaving Bellwood is quite touching, even for those who don't like them leaving. Especially the hug and exchange between Ben and Gwen:
Gwen: Take care of yourself, Doofus.
Ben: You too, Dweeb.
Rook winning Ben's friendship when he gets him chili fries.
During the fight against the Megawatth-powered mecha, Rook get knocked out and thrown away. Ben interrupts the fight to check if he is okay, and express sincere concern for him in the process.
Ben (as Gravattack): Rook! You're okay? Come on, partner!
The Megawhatts being freed thanks to Ben. One's being stroked by a Plumber Agent in delight. Aww...
The Galvan species accidentally created the Galvanic-Mechamorph species, but rather than react in a hostile, aggressive manner, they welcomed the Galvanic-Mechamorph species and acknowledge the moon that they experimented on as their home.
Am I the only one who finds Khyber's behavior to his pet kind of nice? He's literally petting the dog, treating his pet with kindness and respect.
Got that right. He even calls him "friend."
Even in "Of Predators and Prey", despite a lot of references to him being gotten as a means to be a Nemetrix user, Khyber still seems to legitimately care for it, as after his ship is destroyed, he pets his dog after he whimpers, saying that everything is gonna be fine.
Next time we see them the Nemitrix is malfunctioning, and the dog is going berserk while randomly transforming. Khyber is just restraining it while trying to calm it down. It's clear he won't harm his dog.
Which makes it all the worse when he ditches his pet, taking the Nemetrix with him, when the odds turn against him in "Showdown". Fortunately this sets up a heartwarming moment later.
Gwen and Kevin smiling while Rath rants at them. It's made quite clear they've missed his tirades.
Ben and Rook have shown how far they've come since episodes 1 and 2:
Ben: Guys, this is Rook. I don't always get him, but he's cool!
Rook (smiling): The feeling is mutual.
A small one is when Ben and Kevin can't tell if Gwen was hurt by the missile that hit Kevin's car. When the dust clears Gwen looks to them and gives a small smile, which Ben returns right back. It's small, but it's nice to see.
How about the fact that Rook arrived at the scene of the attack mere moments after it happened? If he was at the Plumber's base letting Ben do his own thing like in episode 4, then there is no way he could have got there that quickly. The only explanation? Rook had been there the whole time. He just kept hidden so that Ben could catch up with his cousin and his best friend.
The part when Ben got the grasshopper smoothies for Blukic and Driba. Yes, technically he was using his fame to his advantage, but considering how many smoothies he and Rook had apparently gone through in comparison to Blukic and Driba, and what little money those two would have been able to carry on them, it was certainly a nice gesture from Ben. That and how he says to bring him along next time, when doing it this once had him and Rook in serious trouble with Trumbipulor.
In "Ben Again", 16 year old Ben talks to 11 year old Gwen. Does he tease her and insult her? No. He tells her he misses her (she's in college, and happily tells her she got in early). He's polite and mature to her, even if Gwen doesn't fully appreciate it.
The ending of "Store 23". Ben gives Grandpa Max a hug and tells him to never stop yelling at him.
Speaking of Grandpa Max, Ben 23 reveals that his Grandpa Max died before he received the Omnitrix, and he says he misses him. It goes to show that despite having his ego inflated worse than Ben 10's own, he still cared for his grandfather and truly misses him.
Even better, throughout the episode Ben 10 acts as a mentor to his counterpart. Even better When he has to leave later on, he does so leaving Ben 23 in the mentoring of Tetrax, Azmuth and Six-Six.
In "Showdown", Kevin rescues Khyber's pet (whom he had ditched earlier when the odds were against him) after it gets trapped under debris. The pet repays the favor by pushing Kevin out of the way of more debris. At the end of the episode, Kevin has adopted it. He's even the first to notice that it's a female.
And after Malware killed Feedback, Azmuth personally went to visit Ben in his home, trying to encourage Ben not to let his loss define, but to learn from it.
In "Tummy Trouble" Ben and Rook both get into an argument and take sides with the populace in what course of action they should pull. They both go with their faction, but instead of turning it into a competition to see who's better, Ben and Rook, sincerely wish each other luck, and go to help the people instead of fighting to prove the other wrong.
In "Many Happy Returns" Gar (Looma's Father) mockingly calls Ben "Earth's greatest warrior". Rook corrects him by saying "Earth's greatest hero." Considering what happened in "Of Predators and Prey" parts 1 and 2, this shows something of a shift in Rook's attitude.
In "Vilgax Must Croak", Max reassuring Ben that he did his best as Ben is berating himself for his failures. He's just relieved that his grandson is still alive and well. Contrast this with the dynamic between Milleus and Atea, with Atea trying to downplay her failure and Milleus caring more about her screw-up than he does about her well-being. Keep in mind that both of them were extremely lucky that Vilgax came down with a case of Bond Villain Stupidity and didn't kill them when he had the chance.
In "While You Were Away", Rook's father finally gives him the "Well Done, Son!" Guy moment he deserves, even going so far as to say that he's become a hero while he was away. Young One reuniting with Shar halfway through the episode certainly counts, as does Shar herself wanting to follow in her big brother's footsteps and become a Plumber.
Not to mention Rook's response at that last revelation. He gets Ben to write a letter of recommendation for Shar into the Plumber Academy, knowing how much influence Ben has.
Mr. Baumann may be a jerk, but he shows he has a heart of gold by helping house the Resistance during the Frogs of War two parter.
Fan reactions have been mixed, particularly among Ben/Julie shippers but Julie's new boyfriend is adorable. Even if you don't like him, you have to admit the way he continues to attempt to defend Julie, despite getting repeatedly knocked on his ass, not to mention the way he gets into her Action Girl moment as she's fighting Looma, even going so far as to take a few snapshots, is pretty damn sweet. All in all, he's a nice guy who supports her hobbies and genuinely cares for her well-being—so, pretty much just the kind of boyfriend Julie deserves.
In the end of the episode, Ben and Julie decide to just be friends, showing that they still consider each other good company.
Ben and the Saturdays posing for a picture at the end of T.G.I.S., right after Ben had offered Zac a chance at the spotlight.
Ben's relationship with his mother. Even though we only see brief moments of it it's clear that they love each other and that she's a Good Parent.
Seeing how upset Rook was when Ben got captured was rather heartwarming, actually, and his uncharacteristic aggression about what to do should they meet Albedo instead just cemented how much he's grown to care for Ben.
Despite the fact that Ben found the little Transylian girl Viktoria kinda creepy he is actually rather polite to her. He, for the most part, words things carefully so he doesn't upset her, uses himself as a human-shield at one point, and (upon realizing she has a "little kid/ puppy dog crush" on him) tries to let her down as easily/nicely as possible. Even when it turns out she only had a crush on him because he was breaking out (which apparently makes Ben look attractive to the people of Anur Transly) and acts bratty to him once his face clears up he just kinda shrugs it off and lets her go on her way.
There's also the implication that Rook eats at Ben's house semi regularly with his [Ben's] family. Even if you find some Ho Yay in this you can't deny that Rook has become part of the family!
Kevin telling Servantis that Ben is his friend...more than that, a "brother he doesn't always deserve."
Rook's younger brother naming himself after Ben.
Both Hex and Gwen showing concern for Charmcaster and her mental condition, both trying to help her (it doesn't work, but it's nice to see that they care.)
Both the future versions of Kai and Ben hugging when she finds the sphere they thought was gone forever. Even if you don't ship them you can't deny how sweet the moment was.
Also, Kai and Esther bonding, bordering on Les Yay when it reaches this moment◊ when Kai has broken down crying and Ben is about to reach over to comfort her, but stops in hesitation. Esther, who had previously been a Clingy Jealous Girl over the Ben/Kai situation, actually shoots Ben an angry glare for this and wraps her arm around Kai comfortingly instead.
The ending of "Third Time's a Charm". Charmcaster is trapped in her own bag and now kept in Gwen and Hex's library, with Gwen saying that she always wondered if she and Charmcaster could be friends under different circumstances, and now she knows they can be, even petting the bag with Charmcaster in it fondly. It's sweet that Charmcaster is in the custody of two people who care for her and will help her get better.
While she doesn't get any lines, what we see of Charmcaster in "The Most Dangerous Game Show" adds to this, as has been released from her bag, no longer appears to be suffering from any psychosis, and Hex not minding her being in his library indicates that they've had their reconciliation. Helping the other girls save Ben in the end is just the cherry on top.
"Final Countdown" featured plenty of them:
Rook deputizing Fistina as a Plumber (temporarily) and then proving herself worthy of becoming one for reals.
When it looked like the base would self-destruct with everyone in it as they go into space, Rook gives a It Has Been an Honor to Ben. Ben's smile says likewise.
Rook getting promoted to Magister. He earned that and Ben couldn't be happier for him.
The ending of "The Most Dangerous Game Show": After 5 episodes of bickering back and forth, and of Kai constantly denying being attracted to Ben in any capacity, Ben and Kai have a rather sweet accidental kiss and then run off together.
And instead of a painful parting with Esther that would break her heart, Esther gets to call if off with Ben first and reveals she has a new boyfriend, Antonio, who she's genuinely excited and happy with.
Also, all the girls, even the villainous ones (like Attea, Charmcaster, Rojo and even Swift of the Rooters), teaming up to save Ben from the Way Bads in the Null Void. They had a perfect hiding spot so they didn't have to do it, but they did because Ben came to save them and they all were willing to return the favor.
In "End of An Era", when Ben 10,000 bring an arrested Animo to the Plumber base, during Max's retirement party, Animo is aware of Max's retirement and says the place won't be the same without him, and it actually sounds genuine. Somewhat neutered later when Animo shows Max what a Jerk with a Heart of Jerk he is.
Likewise, we see a lot of familiar faces visiting for the event.
In "A New Dawn," seeing Skurd so happy that he is no longer the only known one of his kind is joyful. It crosses into Tear Jerker when he decides to join his ancestors to spread life throughout the cosmos, he and Ben parting, both of them saying they owe one another's life.
The final line: "We're going on a road trip!" A great Call Back to the Original Series.