After Starscream makes his ultimatum, Optimus struggles having to decide giving up the Allspark or Earth.
Optimus: Maybe Ultra Magnus was right. Maybe I'm not programmed to be a hero. Prowl:You're not alone. A wise 'bot once told me a machine is stronger than its component parts. Only I had to learn that the hard way. [Team Hand-Stack]
Ratchet swallowing his pride and apologizing to Wreck-Gar for calling him names earlier. Then giving the confused bot a heartfelt speech, convincing him to become a hero.
After that (once Wreck-Gar's dispossessed of the Microbots) the pair stand side-by-side and smile at each other triumphantly. It was only for a split second, but it sure was heartwarming.
In the episode "Return of the Headmaster" when Bumblebee and Bulkhead finally ask Sari if she's okay after she's lost her father and doesn't know if he's alive, had her family's company been taken away from her, been kicked out of the only home she's ever known, had Tutor Bot and Sparkplug confiscated as company property, and to top it off been informed that there is no legal record of her existence. Sari explains as much angrily, then bursts into tears. Having seen this before, Bulkhead comments that her eyes are leaking. Bumblebee picks her up and says:
Bumblebee: You let'em leak as much as you need to. We're here, and you're safe. So whatever it is, you can always talk to us. We'll listen.
The reconciliation between Sari and her father in spirit, at the very least at the beginning of Season Three after he stands up to the Headmaster, who was currently piloting Starscream, was just adorable.
Further addressed in "Human Error, Part I", when the Sumdacs open Christmas presents. While Sari was a little miffed at the Soundwave doll, she gets a much better gift: a scooter that transforms into a jetpack. She even says "Thank you, daddy!", showing that while she and Issac have had difficulties in the past, she's now fully accepted him as her father.
Omega Supreme: I am Omega Supreme. I am yours to command. I am your pupil. Your dependent. Your obedient servant.
Ratchet: I am Ratchet. I am... your friend.
At the end of the series, the reaction Omega Supreme gets when he reveals himself to the Autobots. He transforms into robot mode and the crowd stops cheering... only to start cheering even louder. Keep in mind that the Supremes were one of the contributing factors to the Autobots winning the Great War, and afterwards everyone had been (falsely) told that Omega had been melted down into scrap.
The flashback to end of the Great War, with Ratchet having to reassure a weakened Omega.
Omega: You taught me to defend like an Autobot, but all I did was destroy like a Decepticon. Ratchet: We do what we must, even if it sometimes doesn't make sense. Omega: I don't understand. Ratchet: I'm not sure I do, either. Just rest now, friend. You've earned it.
This exchange between Optimus Prime and Sari. (at the very end of the series no less, a definite show of how their relationship has changed)
Sari: I know, I know. It's too dangerous. It's always too dangerous.
Optimus Prime: I was going to say, it's more important for you to protect your father and your fellow organics.
Sari: (sheepishly) Oh. Sorry.
Human!Prowl playing peek-a-boo with a baby in "Human Error, Part 1." It's brief, but very cute.
Near the end of "Endgame Pt. 2", it looks like Prime is about to go down with Megatron (Megatron even states that he'll be happy to go down if he can take Optimus with him). Then, just as Megatron is holding Prime up against the Allspark Shield. A now ghostly Prowl appears to pull Prime out of Megatron's grasp to safety.
The final scene, where the entire crew is being cheered by a huge crowd of Autobots on Cybertron.
No love for Prowl saving the Dinobots from being melted down? He's also the most patient with them and always insists on talking when they're acting aggressively. Kudos to Bulkhead helping him save them, too.
Anything relating to Arcee is either this or Tearjerker. Especially when she's rescued by Ratchet and Sari.
A deleted scene at the end of "Endgame" would've had Slipstream revive Starscream with a piece of her own Allspark fragment, despite having little practical incentive to do so. Looks like she didn't hate him as much as we thought.
The intended series finale would've had not only every Autobot ally of Team Prime work with them to protect the Earth from the Decepticons, but also the Dinobots, Blackarachnia and her Predacons (implying she at leastfound closure if not having undergone a Heel–Face Turn), and Slipstream and her Decepticons (implying that for all she may be, she still sees the Earth as her home).