The Touch by Stan Bush is with out a doubt THE Crowning Music of Heartwarming of 1980's rock: Unapologetically encouraging you that "You're at your best when the going gets tough!! You've been put to the test, but it's never enough." Makes you want to be a hero just listening to it.
Kup telling Rodimus Prime "I knew you had potential, lad".
Even more touching if we consider the scene– heartwarming in itself – when Hot Rod rescued Kup from the giant metal squid-like creature and patched his injuries.
Soundwave carrying Megatron to the shuttle after he was badly injured made me tear up because of what it said about how loyal Soundwave was to his leader. Especially since Megatron looked rather pathetic, begged him not to leave, and Soundwave replies with a succinct, "As you command."
An often overlooked moment is Ultra Magnus' actions on Junkion. Having watched all but a small fraction of the Autobots be wiped out and not knowing if Hot Rod's group was still alive, orders the others to fall back as vast numbers of Decepticons appear. As they do he turns and fires at an overhang hiding his friends from the attacking forces and preventing them from helping him or being reached by the Decepticons, then turns to fight them. He lasts about five seconds.
Hot Rod and Arcee being caring and protective to Daniel.
When the Decepticons launch their attack on Autobot City and take down Lookout Point with Daniel and Hot Rod still on it, Hot Rod's first instinct is to protect Daniel.
When it looks like all hope is lost, the Matrix finally opens and we hear Optimus speak.
Optimus Prime: Arise, Rodimus Prime.
Hot Rod: ...Optimus?
...Rodimus Prime is born.
Kup sitting down and telling one his war stories to the Dinobots has a very grandfatherly feel to it. The Dinobots also play the role of excited children very well.