Miko hugging Bulkhead (his finger anyway) when he comes back fine after the final battle in the pilot.
Jack's concern for Arcee, when she is almost killed at the end of "Darkness Rising".
Arcee (weakly): Jack... really? There are other motorcycles in the world.
Jack: But you're my first.
The normally stoic Optimus offering to bring Raf a snowball back from the Arctic in "Scrapheap".
Prime holding Arcee's hand when they thought they were about to freeze to death.
Even when he's on the very verge of death, literally stumbling to reach the Groundbridge, when Optimus sees the swarm of Scraplets heading towards him and Arcee, he immediately places himself in front of her without hesitation.
Arcee allowing Jack to take Sierra for a ride at the end of "Speed Metal".
Arcee calling Jack "partner" after a huge battle with Airachnid in "Predatory". The sun rising helps.
Raf explaining that Bumblebee is like family to him. Ratchet seemed to smile at this, to give you an idea.
Jack reconciling things with his mom, and introducing Arcee to her for the first time.
In "Rock Bottom", Miko trying to dig herself and Bulkhead out of the cave while Bulkhead holds up the ceiling initially comes off as rather cute. However, when Miko starts running out of air to breathe, her insistence on continuing even as she's risking her life really shows how much she cares about the big guy.
More Tear Jerker material as Starscream arrives and threatens the two... Bulkhead tells Miko to RUN, but she just shakes her head and hugs his foot. Then Jack arrives in the drill vehicle and Bulkhead tells her again to get out of there... and she's in tears as she finally gives in and grabs Jack's hand.
YMMV on this, but Starscream having Soundwave record him while he talks about how he has decided to give up on his ambition to become leader of the Decepticons might count. Considering the fact that Soundwave and Starscream, while civil for the most part, don't see eye to eye forobvious reasons, and the fact that Soundwave technically doesn't even have to record it, it's somewhat touching that he would do that for Starscream. Even more so when you remember what Starscream tells Soundwave afterward.
Starscream: Thank you for listening, Soundwave.
The Autobots saving Raf's life.
Ratchet admitting that he has grown to like Raf. It shows he's not as much of a jerk as he first seemed.
Miko hugging Raf might be small, but it shows that she cares for her friends.
Optimus' little smile to Raf when they were both recovering was adorable.
June and Jack hugging in "One Shall Rise, Part One". It shows she acknowledges that the Autobots save lives. She does ground him for nine years, however.
"One Shall Rise, Part Two": Bulkhead, Arcee, and Bumblebee all vowing to protect humanity for the sake of their human friends.
Optimus entrusting Jack with the key to the ground bridge power supply before entering Unicron. Their talk in and of itself is great, with Optimus himself acknowledging that Jack has matured enough and earned his trust.
Without spoiling anything, one scene of episode 26 makes it even more heartwarming.
A slightly less notable scene due to all the action and fast paced story is when Ratchet immediately shields the kids in the building when a serious earthquake hits. Fowler and June are left out in the cold, but Ratchet can't stretch that far (and it's later revealed that they moved to join the kids anyway).
In a meta-example, during a panel at BotCon 2011, Josh Keaton (Jack's voice actor) admitted that he'd never owned an Optimus Prime toy growing up. Before the panel ended, someone had found him one (admittedly not a difficult task at a Transformers convention). Peter Cullen even signed it for him.
Jack suits up and heads out to Cybertron. The "goodbye and good luck" bit between him and the group really shows how close they've all become.
In what has got to be some of the most hilarious Mood Whiplash ever, a Star WarsShout-Out leads to one for Breakdown, of all bots. After reading what he believes to be a Vehicon (actually Fowler) the riot act for missing a check-in, Fowler repeats Han's oft-parodied "How are you?" line. Breakdown is initially taken off-guard, then tells Fowler that he knows they're doing a thankless job and encourages him to keep up the good work.
The following exchange from "Orion Pax, Part 3".
Optimus Prime: Hello, Rafael.
Then there's Jack using a fully-charged Key to Vector Sigma to restore Orion Pax's memories as Optimus Prime
Orion Pax:(Sees the Key in Jack's hand) Are you...certain I am worthy?
Jack: You have no idea.
Easy to miss, but as Jack and the bots return to base, Raf runs up to Bumblebee and gives his foot a big hug. D'aawwwww!
In the "Orion Pax" three-parter, we witness the Character Development of June from an overprotective mother-hen into a parent who trusts and has faith in her child Jack. What mother wouldn't be proud of watching her son grow into a brave warrior and responsible adult before her eyes?
When Ratchet picks Raf up from school in "Operation Bumblebee, Part 1", he sees that the boy is upset and offers to let him ride with the siren on. Raf declines, but it was a nice gesture, all the same. (Also counts as a funny moment.)
Ratchet also does a good job of comforting a self-deprecating Optimus, telling him not to take Megatron's words about what he may have done while he had amnesia seriously.
The lengths Ratchet is willing to go to to help Bumblebee. He immediately and without hesitation offers to donate his own T-Cog to Bumblebee when retrieving Bumblebee's own T-Cog doesn't look possible any time soon. He ends up not having to do so, but he got as far as being there on the operating table anesthetized so Arcee could perform the surgery in his place.
The reason why they don't follow through on the transplant after Bumblebee's cog is horrifically damaged: Bumblebee won't accept it.
And then there's Bumblebee's utter joy when Ratchet is able to successfully repair and reinstall his T-Cog, giving him back the ability to transform. The first thing he wants to do? Go out for a nice long ride with Raf.
Ratchet's delight is pretty palpable too, especially that first smile he gives.
Optimus and Wheeljack telling Dreadwing they'll gladly face destruction with Bulkhead, who currently had a bomb strapped to his chest. Autobots stick together until the end.
The fact that Bulkhead thought he was going to die and tried to keep Wheeljack away from him in an effort to save him.
Deep down, Bulkhead's just a big cuddly ball of heartwarming. This episode just brought it to the forefront. "Sorry, fishies!"
Near the beginning of "Nemesis Prime" we see Jack, Miko, and Raf racing cars with their guardians (Arcee, Bulkhead, and Bumblebee) cheering them on. Something's just really sweet about seeing these characters who are often in very serious situations have fun once in a while.
Plus the fact that Raf, the youngest and smallest by far, is handily kicking their asses.
Ratchet saving Jack in "Flying Mind". Anybody else could have got him, but Ratchet saves him anyway to make sure.
The end of "Triage" has Ratchet and Wheeljack earn the other one's respect. It might not seem like much, but considering it's Ratchet and Wheeljack, it says a lot.
Ratchet:"I am glad... that I had you as backup, Wheeljack."
Wheeljack:"See you around... Ratchet."
Ratchet's sheer joy at seeing Project Iacon data now flooding into the Autpbot base.
"Rafael, you're a genius!"
Ratchet and Raf working together on the virus. It's just one more display of how much Ratchet has come to care for and respect the kid.
Soundwave gets one, as well. He's got Wheeljack at his mercy and is about to finish him off, but stops and flies off the moment he gets an S.O.S. from Laserbeak. It's actually kind of endearing that the silent bot would give up such an ideal opportunity to go help his drone.
"Toxicity". Bulkhead, seemingly ready to check out after being wounded by Hardshell, and poisoned by Tox-En, gets back up and soldiers on after being reminded of one thing: Miko.
His interactions with Fowler are also heartwarming, especially when Fowler talks about his past as an army ranger and Bulkhead states that they're Not So Different.