Edit: Comment with your recommendations!
Examples:
Hotel
Adou
Majime na Jikan
Scientia
Kakutoshi no Yume
Ikigami
Coulomb Fille
Ibara no Ou
Mahoutsukai ni Taisetsu na Koto
Hajimari no Hako
Purple Qualia

JUST ADDED!! (01)
Robot
Straw

Speculative fiction doesn't need to be thematically or with a main genre being Sci-Fi or Fantasy. Subtle elements are enough, so long as they bring a kind of drama to the story than modern life can't.

I don't want to be too specific about this. The only criterion I'm somewhat more serious about than others is that the work is good (obviously, you're vouching for it 😀 ), and relatively little known.

Also obscure one-shots and anthologies or collections of short stories are especially welcome. But keep everything else coming too 😀

Little known where? Doesn't matter. If it was a surprise find for you, list it. Mention why it was surprising, or whatever you want to say about it 🙂

Now to the guiding list. Stuff I've seen that sort of fit what I'm looking for:

(The following list is in no particular order. And some titles on it may be well known to enthusiasts to non-English communities.)

surprised you don't have Canaria-tachi no Fune on that list

Quote from carcar435867

surprised you don't have Canaria-tachi no Fune on that list

Looks great! Thanks man 😀

Wait... I was asking for recommendations. Is that unclear? Is that why no one else has responded yet T_T

A few speculative fiction works that I've enjoyed over the years... some have mild supernatural elements while others have full-on fantastical settings but all of them have a "human twist" imo

Series

Mia - Unjou no Neverland
Aozora to Kumorizora
Neko ga Nishi Mukya
Wakusei Closet
Asamiya-san no Imouto
Death Sweeper
Ultrabaroque Deprogrammer
Toumei Ningen no Hone
Alice from Hell

Oneshots

Denpatou
Earthly Paradise
The Watchman
World's End Sabotage
Kuragehime (UKI Atsuya)
Ito mo Tayasuku
Black Cat Tunnel
Comic Hoshi Shinichi (Anthology)

I'd highly recommend going to Lovely Strange Dark's website and looking at more of the titles they've picked up.

Nice list, thanks!

Lovely Strange Dark look great. Eerily close to my query in what themes they usually cover. Lovely (human), Strange (speculative), and Dark (both).

baiyang gave a lot of great recommendations, including the one for LSD's projects. Seconding Neko ga Nishi Mukya and Wakusei Closet in particular. (Actually, all of Tsubana's stuff is great.)

I'm just going to throw out a recommendation for any of Mozou Crystal's stuff too, especially her Spectral Wizard. I've been having a lot of fun with Girls Dictionary lately as well.

Ishiguro Masakazu's stuff is pretty great too. I think his Tengoku Daimakyou fits your request pretty well.

And, if you haven't read any of Douman Seiman's work, you have got to try at least The Voynich Hotel. It's pretty different in tone from the rest of these recommendations, but it's super fun, and Douman's style is... singularly unique.

Oh, and Saturn Apartments if you haven't read that yet.