These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
One of Fran's employers was a vain scientist who sought out eternal youth. In the pursuit of said eternal youth, she was shown to be very intolerant towards any doctor who failed her, and would punish them by decapitation and would steal their research on top of that for the sake of turning profits. Not just monstrous to the doctors she hired, she also had a thing for slaughtering clones of herself for the sake of drinking the juice from their eggs.
The psychotic serial killer and serial rapist known as the "Very Lucky Man" was known as such because of his advanced healing factor. Thanks to said healing factor there was no way for him to be executed, and knowing this, he defiled and slaughtered as many people as he could manage.
Evil Is Sexy: The only one of the Madaraki sisters to be indisputably evil, Gavrill also has the most fanservice-laden chapters and has the most voluptuous figure.
Family-Unfriendly Aesop: It's not known whether the author intended to put them in the story, but there are still subtle messages. The most obvious one is in chapter 23 Justice, where a man gets modified by Fran into a super hero named Sentinel. He starts killing criminals, only to be hunted down later by the relatives and loved ones of those he killed.
Well, it's a deconstruction of the typical Toku program. The hero, by using Fran to become stronger and stronger, eventually morphs into a toku-esque monster, who is then attacked by new Toku-esque heroes, who are then augmented themselves... and so on.
Veronica might appear to be a ruthless killer, but she actually has a good heart and the moral responsibility to at least grant quick and relatively painless deaths. Plus she looks really, really cute.
In chapter 30 the people who get off on nearly killing themselves manage to squick out Fran herself.
Tear Jerker: Chapter 38. One of the few times the final result of Fran's work is not played for Nightmare Fuel.
Also in the ending of chapter 43, where a rich girl's uncle who formerly came to Fran for a brain transplant ended up sharing a body with her due to an "incomplete" operation. When a bomb goes off in her house and several people who were after the inheritance she received were killed, the uncle has his own brain put in the girl's old body while he made Fran put the girl's brain into a clone of her. The other people who got killed ended up sharing the old body along with him, as was the uncle's wishes just so that the girl could live freely.
Chapter 25 when Veronica is almost sold to a pedophile group by the only friend she made on school. The saddest part? She knew it all the time, but stuck around as the girl was the only one at school who treated her nicely. And at the end, Veronica said the only phrase that can be used to comic relief and heartwarming at the same time: I'm not crying...I SAID I'M NOT CRYING!
Chapter 48. The somewhat Sympathetic Murderer Nogizaka finally finds happiness... comatose and dreaming of a fantasy world where, finally, there are people who love her. Come to think of it, this fact is what makes said character sympathetic.
Okita, the cat with a guy's head. Said head (if you ignore the cat body) is actually quite handsome, as demonstrated when Okita used a puppet human body. Many of Fran's other creations also count, such as her dog-headed butler.
Adorea. She's got one hell of a tragic backstory. She's also a very sweet girl... when she's off the clock anyway. Only Franken Fran could make a tentacle faced man-eating organ harvesting Humanoid Abomination into a Woobie.
Veronica, if you consider that she passed through quite a hell after she separated from Professor Madaraki and before she found Fran: Having a dog as her only companion (which very likely have died), being scolded as a freak and constantly targeted by the mysterious organization that wants the professor's secret projects. Not to mention the bad things that occasionally happen to her, like the bullying she had to endure in chapter 25 - though in that case she came off as an Iron Woobie. Also, Fran apparently likes to take her apart and do...things to her.