The first thing that comes to mind is Mieri Hiranishi's work; i used to read chapters as she posted them on twitter, and she focus her story around butchness a lot. But I would also really recommend Oniisame Ee.., by Riyoko Ikeda (I havent read Versailles no Bara yet..), Double House by Haruno Nanae, Free Soul by Ebine Yamaji.. the memories of reading these stand out to me!
I also only watched the anime (and it wasnt perfect, but oh well) but i would like to name Kageki Shoujo!! as a work that presents gender and girs' love in a very interesting and fun way.
hope this helps :3