So… I knew 魔法 and I knew 瓶, they are frequent enough to learn early on. But when I ran into 魔法瓶 it did not make sense in context, because this wasn’t that kind of book 
Of course, it’s something altogether different… although it too is kind of a magic bottle: thermos bottle, vacuum flask 
not the most recent but the most interesting one i encountered lately : 皮肉 (ひにく、irony)
i like it mostly because of the crazy etymology of “skin + meat” → shallow, no content → superficial → sarcastic → ironic
Now just wait until you encounter マジックテープ
Yes, yes… I’ve had the pleasure already 
Reminds me of the Harry Potter series’ school for Japanese wizards- Mahoutokoro. Magic. Place. Cmon Joanne.
お河童 - bobbed hair (because the style looks something like the mythical kappa’s hairstyle)
This’ll be an easy one to remember.
好むと好まざるとにかかわらず - whether one likes it or not
Not a difficult one, just didn’t know until now that they’d use the same expression…
(Although it’s from Murakami so maybe… not something they actually use regularly, just his unusual choice of wording?)
I found it in something else I’ve read before, but… it was also from Murakami 
The sentence:
これまで私は、自分は生意気で身勝手なところはあるにせよ、決して傲慢な人間ではないと考えてきた。しかし「自分の置かれている立場は、好むと好まざるとにかかわらず、発生的にある種の傲慢さを含んでいるものなのだ」という基本認識をより明確に持つべきだったと、今では反省している。
(アンダーグラウンド)
盲亀浮木
Reading: もうきふぼく
Literal meaning: blind turtle and a floating piece of wood
True meaning: unlikely, rare event
Origin: a story told by Buddha about “how good it is to be born as a human”. It’s also the origin the expression 有り難い, it’s worth reading it.
直感 ちょっかん intuition
飛ばし読み・とばしよみ・skim reading, skipping through text
Thought this might be a very useful word and easy to remember
微妙 (びみょう)
意味 - subtle; difficult; doubtful
I learned this one from 安達としまむら, the author seems to like using this word as it comes up quite a lot.
ウズウズ・itching to do something, impatient, sorely tempted, eager
例文：誰かに話したくてウズウズしていたのだろう。
蔓延る・蔓延する
to spread (negative, eg. disease), to run rampant, to proliferate
例文：田舎こそ不法就労が蔓延っている。
Translation: Illegal labor practices are especially running rampant in rural areas.
親戚 relative
There’s a cluster of very similar words to 蔓延る/蔓延する that I’ve run into that I had to look up the nuances of:
瀰漫 - often used for intangible things like trends or mood/atmosphere, and for certain medical conditions
猖獗を極める - limited only to bad things at the height of their bad state
氾濫- originally used for flooding, it can also mean a spread of bad things
Other than 氾濫 these are pretty niche, but can pop up here and there in literature.
My wife didn’t even recognize 瀰漫 and 猖獗 at first glance, so that’s crazy work on your part! What kinds of books are you reading that such esoteric words come up? Are they more common in a specific genre?
Just started reading ８番出口 and came across 有象無象 from the following sentence「親指を下から上へと動かすと、スマートフォンの中で有象無象が次から次へと現れては消えていく。」
Its definition is pretty interesting as well:
有象無象とは 元は仏教語で有形、無形全てのもののことで、この世に存在する全てのもののこと。 または、数が多くつまらない人や物のことを卑しめる言葉。
Reading? Isn’t it a computer game? And a movie? And a real-world puzzle game?
All of those — and a novel!