Heartwarming: Puella Magi Madoka Magica The Movie: Rebellion
The first half hour or so is made of this. While it's a given that things will be dark and horrible once the plot gets into motion, for just a little while, all five girls and a former witch are happy together, living out a sugary sweet (if immensely trippy) conventional magical girl series.
The Flower Field. Madoka cuddling with Homura is heartwarming enough, but then she starts braiding Homura's hair. It's for both how much Les Yay there is in that scene, and the pure symbolism in the act. Becomes a little less heartwarming on a second watch-through, however: it's possible to pinpoint the exact second that Homucifer is set in motion.
Sayaka telling Kyouko that she regrets leaving her behind when she died. It's pretty close to a love confession really, and if you look closely, it was enough to bring Kyouko to tears. Well, a tear.
Mami and Bebe/Nagisa's relationship. Bebe even drew a picture◊ of Mami!
The whole fight between Homura and Mami happened because Mami was trying to protect Bebe from Homura.
Homura finally becomes a witch and is aiming to kill herself. But then the magical girls show that they're not going to give up on Homura no matter what.
Oktavia doesn't really fight Homulilly. Instead she grasps her hand, almost if to say "Don't worry, everything will be alright."
The Law of Cycles has fallen. Madokami is powerless. Homura has become a god, trapped Madoka in a Gilded Cage, and declares that she and Madoka will become enemies if Madoka doesn't stop trying to sacrifice herself. The audience is left gawking. Nothing Is the Same Anymore. But then Kyouko is seen at school, eating Pocky happily with Sayaka. Mami saves Nagisa from an avalanche of cheese, ensuring they meet and Mami has the friend she yearned for. Kyosuke's hand is healed even though Sayaka is alive: despite how much Homura and Sayaka don't like each other, Homura took the time to make sure Sayaka's wish remained fulfilled. Even after everything, even after Homura's fall from grace, even though she has declared many times she didn't give a damn about anyone but Madoka, she still took the time to give the others their dreams in the new world. Even though it may have be done just to ensure the girls will be too busy with their happy lives to try and ruin Homura's plans.
They finally got their cake. And it's marvelous!
Amusingly, (and heartwarmingly, since it was due to Homura's involvement), it is marvelous and covered in pumpkins.
All In The Manual example, the Anthonies are lend by Gertrud herself. Before sending them to battle, she put a medal (said to be her treasure) on each one of them; remember that before this, she already personally put on their mustaches because she likes them. And she lends them to Sayaka as the main force to save Homura from Incubators' isolation field. Makes you wondering just what the former Witches do (or to be more accurate, 'did') in their Valhalla.
One could consider the conversation between Sayaka and Homura (right after Homura's battle with Mami) to be a bit of a Fridge Heartwarming moment. Sayaka tells Homura that maybe the Witch responsible for the "dream world" is not so bad after all, considering that she ensured that they all can lead the lives they all dreamed of, and that maybe Homura should calm down a little. But since Sayaka is actually Madoka's subordinate and they all entered the barrier willingly, Sayaka knows full well the Witch Homura is looking for is herself. Of course, she can't say that to her directly. Basically, in this scene Sayaka is trying her best to reassure Homura that she shouldn't blame herself for what is happening, without actually saying it.
Sayaka is also implicitly saying since Homura wants this world she isn't really a bad person - essentially admitting she was wrong about Homura.
Despite being the one to really let Homura have it at the end, Sayaka meeting up with Hitomi and Kyosuke is very much this, as she greets them more-or-less automatically...and then she stops, tears springing to her eyes. When they ask her what's wrong...
All of the shots of the girls enjoying themselves in Homura's new world are heartwarming in their own right. The crown jewel however, is Madoka: Tatsuya is rushing to give her a hug as the parents look on happily. Although it's established that history is quite different, the subtext is clear: a tearful reunion between Madoka and the family she left behind that was LONG overdue. Nothing Is the Same Anymore? Maybe. But one can't help but feel that somehow, on this front, things are back to the way they SHOULD be.