I'm looking for novels or manga (not anime) in which the female lead is in a relationship / love with another female, while not being particularly about the romance.
Preferably some kind of supernatural / sci-fi / fantasy or the like.
It's fine if it's only available in Japanese.

Example:
Murasakiiro no Qualia

Gaku and Alice fall deeply in love in many of the parallel universes. However, while it is a very important occurence for the story to move forward, the story is in no way supposed to be a romance.

Check out Engravings of Wraith by Kiera Dellacroix... it's largely about the romance, but, well, it's extremely entertaining. One of the female leads is like James Bond, but more like how James Bond wishes he was in his wildest dreams, lol...

Stray Little Devil - Fantasy-esque, about a world split between Angels and Demons. Shoujo-ai sorta starts there but really picks up.

Pixy Gale - Light fantasy...unfortunately on hiatus with no signs of starting again soon.

@jedinat- Engravings of Wraith seems interesting but x.x"... I'm reading manga / novels to practise Japanese and I can't find anything that suggests it was translated D:!

@wolfinthesheep- Stray Little Devil Already read :3 cute ending
Pixy Gale Dem hiatus' 🙁 ...

Quote from wotonito

@jedinat- Engravings of Wraith seems interesting but x.x"... I'm reading manga / novels to practice Japanese and I can't find anything that suggests it was translated D:!

Well, you did not specify Japanese novels in the OP.

You should try Saki. Believe me, it is supernatural 😉 😀
I'm seconding Pixy Gale, it's great even with the hiatus...
Maybe Boku no Futatsu no Tsubasa...
Flower Flower (ed: damn, this is discontinued too?)

I can't think of any novels, but I'm sure that I've seen at least a few visual novels matching what you're looking for. Though most of them were untranslated, so I couldn't read them... You can find them with a bit of searching through the tags on http://vndb.org/

"Thus is our treaty written, thus is agreement made
Thought is the arrow of time, memory never fades
What was asked is given, the price is paid"

Quote from jedinat

Well, you did not specify Japanese novels in the OP.

So people could put down non-JP titles they like 🙂 .

@Draconic- Thanks for the website, that'll make things a lot easier xD

Perhaps Murcielago which is more supernatural/fantasy, Desutoro 246 and Gunjou for action. One of my favorites is Centaur's Worries.