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.
Draco in Leather Pants / Freudian Excuse: An interesting in-story example—after reading the Account, Omri practically glamorizes Jessica Charlotte, defends her as a poor helpless Woobie at the mercy of her sister and brother-in-law who was justified in what she did and could never have foreseen the consequences, and even makes excuses for Frederick who is arguably a Holier Than ThouJerkass with Mommy Issues. Patrick, of all people, calls him on this by pointing out the darker side of Jessica's jealousy and Frederick's hatred and nastiness, suggesting that this explains a great deal of why the cupboard's magic seems so "evil", both in what it does to the little people it transports and what its use does to the lives of everyone involved.
Fetish Fuel: The Secret of the Indian features a miniaturized Pat being tucked into a normal-sized lady's bosom, because her shoulder's too slippery.
Ho Yay: A scene where Boone and Little Bear are so terrified of a huge booming noise that they hold eachother for dear life.
Nightmare Fuel: In The Key to the Indian, Omri and co. have figured out how to send themselves back in time to make past toys flesh. Omri's father ends up in a faceless Iroquois doll for a few hours.
At one point in time travel, Omri becomes a piece of fabric on an Indian tent, and when it catches on fire during a raid it begins burning him alive until his friends pull him back to the present.
Tear Jerker: Any of the times Omri and Patrick have to say goodbye to their little friends, but the send-off at the end of the first book stands out especially. Also, the deaths of Boone's horse, Tommy the World War I medic, and Tom the thatcher. Even Jenny's death told in flashback wrenches at the heartstrings.
Values Dissonance: Omri is horrified when he learns Little Bear has scalped thirty men, a fact which Little Bear either boasts of with pride or dismisses as unremarkable because it was something so many in his time did (and was a practice first learned from the whites); Boone isn't surprised when he learns of it, thanks to his prejudices. Omri's eventual rationalization of this, which allows him to still call Little Bear his friend and realize he is not a bad person (or no worse than any in his time) puts things in clear perspective for the reader, even if it does partake of Humans Are Bastards:
Even now, weren't soldiers doing the same thing? Weren't there wars and battles and terrorism going on all over the place? You couldn't switch on television without seeing news about people killing and being killed. Were thirty scalps, even including some French ones, taken hundreds of years ago, so very bad after all?