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 postive emotions is just... well, cute.
YMMV, as he was acting rather off depending on how you see it.
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.