The episode where Jetstorm is about to defect to the Maximals after Megatron's apparent death and Thrust runs in, warning them not to take his only friend. Jetstorm, who is an amazing Jerkass, actually takes the statement seriously. He would make fun of anyone else who showed emotional concern for him. Just ask Blackarachnia!
Thrust: My boss is dead. Everything's falling apart. I won't let you take my best friend! Jetstorm: We're...friends? Thrust:(softly) Why not?
The last episode where Cheetor said that Optimus lives on inside all Cybertronians and meets Primal's spirit one last time as it moves on to the next life.
Rhinox's spark talking to Primal after dying. Rhinox explains that he's free of the Tankor programming and no longer has to struggle against it. Primus has forgiven him and allowed him into the Matrix.
Rhinox: I paid the price for my misguided deeds... But it is not to late for you. Embrace the true nature of your spark.
The end of "In Darkest Knight," where Silverbolt lamentshis actions as Jetstorm - actions that he admits he "reveled in":
Silverbolt: I don't know what I am anymore. Blackarachnia: You are what you've always been – honest, pure, virtuous to a fault. (Blackarachnia takes his hand) Silverbolt: You're taking a huge risk. Blackarachnia: Considering how well I know the goodness in your heart, it really isn't a risk at all.
The final episode is just one big moment of heartwarming with Optimus Primal pretty much scolding Optimal Megatron, culminating in Optimus's speech about the true nature of what life (for a Transformer) is really supposed to be about.
Optimus Primal: We are all but fragments of the Matrix. Which releases each of us in order to struggle and grow and evolve. So when we return it may grow and evolve. Thus we share with the Matrix, not just by battling but also by acquiring knowledge, wisdom, and experiencing love!
Makes you wonder if he was thinking about a few fallen friends when he gave that speech.