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.
Growing the Beard: Under Town was where the series truly started to shine, with continuity starting to come into play and the first mysteries being introduced. And that's not even going into the reveal of the Mason's character, or the bittersweet ending.
Moral Event Horizon: Stephanie definitely crosses this line in Frost Bites, when she arranges for Edgar and Ellen's deaths. She would have crossed it sooner when she buried them underground in Nod's Limbs, except that she was counting on the balm spring keeping them alive, albeit trapped for who knows how long.
Edgar: Stephanie, don't do this! You don't want our blood on your hands!
Stephanie: Of course I don't. That's why I'm wearing gloves.
The loss of the Gadget Graveyard and the death of Berenice. Especially if you watched the cartoon first and got used to having them around. While Status Quo may be God in an episodic show, here, it turns out, is another matter entirely.
The ending of High Wire. After everything has gone south for the twins, they trudge back home and find it's no longer theirs. The illustration of them staring forlornly at the notice on their door is the sad and bleak note on which this book ends.