Snow Light chapter — a possible aversion of a similar Black Jack chapter.
Attempted Suicide chapter. For once, the only person who ended up worse off deserved it.
Cosmetic Surgery chapter. Not only do the girl and the boy now have a proper relationship without her freaking out at his touch, but we see a ton of the students happily enjoying their strange new bodies from their various surgeries.
We later find out that the boy and girl broke up after one of them cheated on the other though...
Beautiful World chapter. The painter who gets eye surgery arguably counts too. Sure, the sweet girl he hooks up with could probably be Saya's sister, but they seem to genuinely love each other, and he goes to thank Fran for his newfound happiness.
Trivial Love chapter. Even bioweapon horrors can find true love.
The Twenty Four chapter, bringing a whole new meaning to the term "Walk A Mile In My Shoes".
There's a rather blink-and-miss moment in Aura chapter, where Fran asks Okita and Veronica whether they had somebody they liked, and Okita answers "You", in a very matter-of-factly manner. Dawww.
The end of the Sea Monster chapter. "Mother. I'm home."
The interactions between Shion and her uncle Akira in chapter 43. After having his brain attached to her to get a hold of her inheritance, he learns just how much her life sucks and willingly has himself placed into an And I Must Scream situation so that she can have a free life.
The company president in Rolling World 2 is so moved by the love that the two runaway mascots feel for each other, that he allows Fran to give them human bodies. Then we see theirnew bodies.
The ending of Left and Right, the re-union of the two halves of Fran was unexpectedly dramatic, but it worked.
In the same chapter, after Fran's left-half angrily insults Veronica, Fran's right half comforts her and tells her how much she appreciates her work.
The very last main chapter, Dream. Seeing every character Fran has ever interacted with throughout the entire series all gather together for her rather symbolic "party"; the epic proportion of the results of all her work, be they good or bad, that stretches across several pages to show. This is her dream, she still remembers them all, and she feels both happy and fulfilled at her efforts. To top it off, Fran finally gets to see her beloved professor, though it's a little sad since it's only a dream. Heartwarming or not, it is an incredibly satisfying chapter to read.
After seeing Veronica get so harshly picked on during most of the final extra chapter, seeing her sisters hug her when she starts to cry is absolutely adorable.