All right, there can’t be just one. But still, if I had to choose one, it would be Gunnm (known in the US as “Battle Angel Alita”) because of the diversity and the richness of the themes. Yukito Kishiro talked about intimacy of the characters and their relationships and also, about broader considerations like dreams, hopes and meaning of life.

There’s violence (quite a lot) but you can always see the author’s goal behind it.