Golgo 13 is one of my favourite mangas of all times: i have the spanish edition of two volumes of the 13 best stories according to the readers and it's a blast, well worth the (re)read from time to time, and a couple of issues published by Leed in the eighties (like an arc when Golgo visits in my country to kill an ex-president). Everything about Duke Togo is shrouded in mistery, but it's more a vehicle to tell things about power, corruption and human drama than a character in her own.

2001 Nights by Yukinobu Hoshino: A thematical mix between the movie 2001 and the One and Thousand Arabian Nights, this manga is a collection of stories set in the distant future, with humanity unlocking a new technology every 100 years. Every story works on her own, exploring many themes of classic sci-fi literatury, the Night Seven (Jupiter Rising) is one of the best parts of the manga.
Sashiki Onna by Minetaro Mochizuki (published in EE.UU recently, with the title Hauntress)
One of the first mangas i owned, it's a really disturbing story about a phantasmagorical woman who stumps in the apartament of a boy. Mochizuki is a master of the oppresive moods, with Dragon Head as another work who ran into the same themes.
Chronowar (Denmu Jikuu) by Kazumasa Takayama:
My first manga: An excellent sci-fi tale who combines romance, body horror, and existencialist themes: a robot impacts in Japan with the mission of learning more about humans, and choose three subjects to experience what is humanity: a cop, a thief and a woman. There's an unrelated sequel, still unpublished to this day.