Good question! She has written lots and lots of stuff, and I’ve far from read all of it, so please take this answer with a grain of salt.
I’m pretty sure that the two books out in English, Heart of Thomas and A Drunken Dream and other stories, contain what a lot of people agree are her best works: Heart of Thomas, Hanshin (16-page short story about conjoined twins), and Iguana Girl (the short story about a girl whose mother insists she is an iguana). These are definitely considered masterpieces.
Another one which is considered her masterpiece, which I haven’t read (it seems like a huge emotional investment), is Zankoku na kami ga shihai suru / A Cruel God Reigns. I’m pretty sure there’s a complete translation online.
My favorite work by her, on the other hand, is Gin no sansaku / Silver Triangle. It leans much more towards the science fiction end of things than the shojo manga end (it didn’t run in a manga magazine but in Japan’s SF Magazine), and has a reputation of being obscure and murky, but I really love it! It’s so dense and perfectly plotted and executed, it’s like a piece of art. If you’ve read A Drunken Dream, it’s a bit like the title story but expanding on the premise of “someone is playing back this exact moment in the history of the universe again and again in order to maybe fix something broken in the universe”. Really fascinating! I also really like her other sci-fi stories, like They Were 11 and Star Red. The other day I read a short story called Nise-o / Fake King which was also fantastic and left a huge impact on me.
I’m sure there’s loads more I have yet to read that’s also amazing, though. :)
What about Takemiya Keiko? (well, out of all 24-Gumi i only have read work from Hagio Moto and Takeimiya Keiko *embarrassed)