From "Doctor K": The entire episode, especially Dr. K's flashbacks to her life growing up at Alphabet Soup, counts as one giant tearjerker. Someone please give her a hug.
From "Ghosts": Dr. K's reaction to seeing Gem and Gemma for the first time since Venjix attacked Alphabet Soup. And she smiles, even with tears running down her face.
From "Ancient History": Dr. K's exchange with Colonel Truman in Corinth HQ.
Dr. K: We all do things in life we regret. But if we don't learn from them, and move towards a brighter future, we pay twice.
Colonel Truman: I've already paid more than most.
Dr. K: I know. And if I could access the space-time continuum long enough to undo what I did, I would. That's not possible.
The deletion of Gem and Gemma is one of the saddest moments in the franchise, right on par with the deaths of Zordon and Kendrix.
The last few scenes of the series has two. One where they were returning their morphers and Ziggy quietly, and not just a little bit sadly, says "Get in gear". And the second where Dillon returns to a flower we saw in the first scene.