Graphic novels are complement to comics periodicals. Where periodicals are the soap operas of the comics world, graphic novels are the movies or mini-series'. Just like their televised counterparts, graphic novels can span fiction, non-fiction, and anthologies. There is a fine line between a long graphic novel and a short series, and I don't know if I can differentiate them so there might be some graphic novels here that could be better placed in the Series section. In the spirit of life though, ¯\_(ツ)_/¯.
Nameless, by Grant Morrison
Nameless takes a trippy journey through cosmic darkness. It is Lovecraft in graphic form, if Lovecraft ever knew about drones, asteroids, Xibalba, and dark intelligence of a cosmic alien intent on psychic invasion on a global scale while masquerading as vengeful divinity. In short, it's a Grant Morrison graphic novel.
Nausicaa of the Valley of Wind, by Hayao Miyazaki
Nausicaa is one of my favorites. It touches environmentalism, the horrors and sometimes necessity of war, imperialism, and spirituality across seven issues. The story itself is set is a post-apocalyptic world that is rebuilding itself after a global man-made cataclysm that destroyed civilization in seven days. Now, an old threat in the form of an ancient killing machine has been found and the remaining nations fight over who gets to use it while the world around them crumbles fromthe sins of the ancestors. It is a beautiful story where the soul of nature is laid bare and the nations' desire for destruction is tempered by the peace forged by the people.