Special mention has to go to Will coming in from a storm in the beginning of the one shot, rushing upstairs and effortlessly putting a fussy Todd who had just thrown a tantrum and hit one of the family servants to bed. When Will goes downstairs, one of the maids comments that Todd must see Will as his father, saying, "He loves you." Will denies it, but you can tell from his expression that it makes him happy. Counts as a Tear Jerker, since Will lost his entire family to tuberculosis.
Todd Allison had been working on a project, but getting involved with the Violet Investigation Unit has put it on the backburner. Due to his kidnapping, he's temporarily forced to take a break from the case, and he's so ecstatic, he smiles, hugs Clancey, and laughs. It's so sincere and seeing Todd, usually quite the sour jerk, express some positive emotions is just... well, cute.
Admittedly very minor, but in chapter 2 Clancey asks Todd if he'll introduce him to Petunia. Todd says no, and adds, "You'd probably frighten her, you beast!" It shows that despite the fact he's unpleasant and hard to get along with, he cares quite a lot for Petunia. In fact, once he gets back to his apartment, he remembers the previous night and goes to check on her in his room. When he finds that she's gone, he rushes out of his apartment in a panic. When he bumps into her as she's leaving hers, he gives a chuckle as he muses that she seems to be okay.
Their whole relationship is rather heartwarming, since she's one of the few people he's actually kind of nice to.
Chapter 12 has Todd and Petunia realizing that Cyril is injured and expressing concern for his health. Cyril, for his part, actually seems flustered before leaving.