Princess Tutu has as many of these as it does correspondingly dark moments, but one of the best comes in Akt 23, when Tutu is kidnapped by Drosselmeyer and the story stops. Then, because of Uzura's meddling, it starts going backwards. Fakir, realizing how much Ahiru has changed him, refuses to go back to who he used to be, and begins to write Tutu's story down for her, pulling it back on course and freeing Tutu from Drosselmeyer's clutches.
Also in Akt 23, Uzura meets the puppet she was made from, Edel, and asks her if that means Uzura isn't real. Edel replies that she was just a puppet, but Uzura is different...and Uzura begins to cry.
In Akt 22, Kraehe is attempting to seduce a new victim for the raven and her target is Autor. As she's taking him to be sacrificed, however, he confesses his genuine love for her - Kraehe has been told over and over again that only her father and the prince will ever love her - and Kraehe can't bring herself to kill him.
Akt 10: Fakir's adoptive father decides to believe in his son after meeting Princess Tutu and allows him to fight to protect Mytho. He sends him off with an embrace; "Go, my son."
Princess Tutu can never confess her love for the prince, or she'll disappear in a flash of light. However, when faced with losing him to Princess Kraehe and leaving him heartless forever, she does it anyway...through dance.
When Ahiru went to such great lengths to protect Pique from becoming a sacrifice for the Raven early in the second season, showing that she truly does value her as a friend and not just a roommate, or one of Those Two Girls.
Fakir: "And even after that time comes, I will stay by your side forever." D'awwwwww!
Realizing that it was the first time Ahiru danced gracefully as a girl and not Princess Tutu.
At the end of the last episode when Mytho asks Rue to come with him to his kingdom and be his princess. When Rue points out that she has the monster Raven's blood inside her he says this.
Mytho: "The story says I'm supposed to love everyone... but right now... I simply want to love Rue the most out of anyone." Cue Rue crying happily and him hugging her. Awwwww!
Early in the series, the first time that Fakir shows some kindness to somebody other than Mytho: when he rescues Duck Ahiru from his locker and gives her bread. Also a Crowning Moment of Funny, because Ahiru almost loves him for his bread.
After Mytho has his heart back, Ahiru turns back into a duck. Every time he refers to, or speaks to her, he still calls her Princess Tutu. Because as far as he's concerned, she's still a princess at heart.
When he first sees Ahiru as a duck, he gets on his knees and bows, acknowledging just how important she is even afterwards.
Mytho: ...That something so small and fragile accomplished this...Thank you, Princess Tutu.
In the last episode, Rue meeting up with Ahiru, who's now permanently a small yellow duck, asking her if she's the Ahiru she knows. The duck nods, and Rue cries and hugs her, thinking of Ahiru and saying she loves her. Ahiru hugging Rue back with her wings and her thoughts of "I love you too, Rue." is the icing on the cake. Awwwww, too!
Fakir promising to never leave Ahiru's side even after she loses the ability to be human, after her worrying for the entire series that people would reject her if they knew she's really a duck.
Also, the last scene in the series is Fakir sitting on a dock near a lake, with Ahiru-as-a-duck floating in the water, showing that Fakir very much intends on staying true to that promise.
Fakir is writing a new story. A story full of hope.
Though the epilogue is bittersweet, with the town returning to normal and no one remembering Ahiru, the scene near the end with Mytho and Rue dancing happily together is very sweet. Rue is not a character archetype that often gets a happy ending. This girl has been used and abused and manipulated her entire life, and had to overcome a lifetime of suffering and being beaten down to set right her wrongs. To see her finally get the one thing she always wanted - someone to love her - is an immensely satisfying conclusion to her character.
Remember the artist girl Malen and how Mytho's feeling of devotion compelled her to draw only Rue? Think about that for a second.