Tying into that, Homura slowly realising she is a witch. Her voice when she says it out loud is so full of grief and despair.
The line "Madoka...thank you for coming all the way to a place like this. I'm sorry I couldn't even say goodbye to you at the end." is truly heartbreaking.
Spider lilies, the flowers heavily associated with Homura's witch form can mean: never to meet again, lost memory, or abandonment. All of these meanings are equally valid for Homura's mental state and equally tragic.
The Flower Field makes it painfully clear that Homura had not found peace with herself and Madoka's sacrifice as suggested at the end of the anime. She kept on keepin' on purely in the name of her friend, but shows a very different truth when given the chance to say with full candor what she herself thought of the situation. And her tone saying those lines is heartwrenching.
Homura: I was so lonely and sad...but no one could understand how I felt! Surrounded by that, I started thinking my memories of you were just something I made up!
Then Madoka tells her that she would never have wanted to leave everyone behind, and Homura crumbles entirely. Those EYES. Her goddamn expression as she realizes the extent of her failure: she may not have saved Madoka's life, but she was content with Madoka's sacrifice so long as Madoka was happy. Now she finds out that Madoka did it out of her sense of duty and was NOT, in fact, happy with her situation. OUCH.
Depends on if the audience buys the idea that the two misunderstood each other in this scene; given that Ultimate Madoka is around everyone, all the time, she technically wasn't far away from her friends at all. Which means that she was okay with her decision, but Homura misreads her and comes to the conclusion that Madoka wasn't happy with her fate. Double oops.
The witch's familiars are reflecting the soul of the Magical Girl. Homura's familiars are seen committing suicide. How much must a girl hate herself to imagine something like this?
After the events of the movie, watching the "Colorful" opening is heartbreaking.
The ending credits sequence. Kalafina's "Kimi no Gin no Niwa" sounds Gothically poignant (in spite of its Yandere-ish lyrics), and the video features outline figures of Madoka and Homura facing each other across a gap. They eventually reach out for each other, and the song ends with them running together into the distance. Of course, this comes just after hearing Homura say she and Madoka will someday become enemies.
On the other hand, there IS a more optimistic interpretation: that after spending so much time with a gap between them, Homura and Madoka may very well reconcile and truly be together. Only time will tell.
Homura's suicide bluff. The look on her face as she pulls the trigger, and Mami's reaction. And finally, Homura raising the gun to Mami's head. Obviously, things weren't quite as they seemed, since fans already knew that Homura wouldn't die from a headshot, and Mami turned out to be a double. And yet, for a couple of seconds, it was an absolutely heart-wrenching scene.
And earlier when they both had perfect kill shots for each other you can see they're both panicked for a second, because they don't want to actually permanently harm the other.
When Homura gives Madoka her ribbons back and tells her that the two will someday become enemies. The manga◊ version◊ of the scene is particularly heartbreaking.
Of the heartwarmingly sad variety, Madoka finally reaching Homura on top of Homulilly's head. When she tells Homura she doesn't have to be alone and she'll always be with her, we have a shot of Madoka caressing Homura's face while the later cries and asks for forgiveness.
Homura's and Sayaka's last meeting after Homura stealing Madoka's god powers resetting of the universe, with the latter confronting the former on why she stole the hope of all Magical Girls. Due to becoming a part of the Law of Cycles and gaining memories of all the previous timelines, Sayaka had gained a deeper understanding of what Homura went through and even sympathizing with her, which could be seen in her interactions with her throughout the movie. She's friendly and amicable toward Homura, and as noted in the Heartwarming page, tried to reassure her that the events of the barrier were not her fault and only proved that she was a good person. During the final battle, Sayaka even mentions that Homura had been working hard and deserved a reward, in stark contrast to her hostile interactions with Homura in the original series where she believed the latter cold-hearted bitch who only cared about herself, only for Homura to prove her initial assumptions right by removing the Law of Cycles, which had granted hope to Magical Girls. The confrontation ends with Homura erasing Sayaka's memories but not before she calls Homura a demon. If Sayaka ever gains her memories back, their relationship is bound to be even worse than it was in canon.
Arguably the last shot we see of Kyubey He's collapsed in a field of flowers on the edge of a cliff, something Homura did to him having reduced him to a battered, frayed, quivering wreck, up to and including his pupils and irises turned broken and ragged, as Homura smugly bandies around the Dark Orb and dances a mock ballet around him. If not tragic for him, it's tragic for the fact that Homura has sunk so low that she turns to what can only be an incomprehensibly excruciating form of torture just to break Kyubey for her own satisfaction when her attempts to keep Madoka placid and at her side become too thankless to stand.
Kyubey is flat out immune to physical and mental abuse. However, in this scene, his appearance might suggest he's scared out of his wits. It would be very much in Homura's character to Kick the Son of a Bitch by making him go through what she and other magical girls experienced - and so, the worst punishment for him would be making him able to feel emotions. Raw animalistic fear would be a fitting reaction once he realizes just how badly is he screwed. Who knows, he might very well feeling remorse and thinking "My God, What Have I Done?"
And even more so, she did it all for the sake of someone who had simply showed her a little kindness. This how broken she must have already been when it all started if she did it not even for a friend or a family member, but simply for the one person who was kind to her. And in the end, she is still doing it all for the same reason she made her wish, to stop that one person from sacrificing herself, because she doesn't want to lose that person, that bit of kindness she got. Let that sink in, people.