Just list the title of the story(s) that you see adapted or referenced very often (just like the title states).

The one I see very often is "Alice in Wonderland" both in adaption and references.

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Cinderella maybe it's really common 🙄

朝露の少女。

“The longer we live, the more weight we carry in our hearts.”

some mangas are adapted from the tales of genji

I like turtles

I see a few Sherlock Holmes stories. 😮

EDIT: Yeah, and a lot of Alice in Wonderland stories.
I also sometimes see general prince-rescuing-princess references.

Romance of the three kingdoms have been referenced in almost all genres of manga(echi, harem, Shoujo, senein, sci-fi etc...).

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Sleeping Beauty a few times, even with male versions.

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But if it makes you happy to win on the internet, have at it.

[color=#FF0000]Screams from the haters, got a nice ring to it. I guess every superhero need her theme music...
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Definitely Alice In Wonderland, you can't believe just how many are out there

Journey to the West, and Romance of the Three Kingdoms.

And the Bible.