I love Japanese manga. Admittedly I don't read it as much these days as I used to, but I still pick up a new series every so often when I have time. Living in Japan certainly makes that easier, with great stores like Book Off, where I can buy used copies for as little as 100 yen ($1). So here are some of my all-time favorite series, as well as a couple lesser-known titles for those of you who are already well-read manga fans.
Revolutionary Girl Utena - by Chiho Saito (少女革命ウテナ). This might actually be my favorite manga ever, although that's a pretty tough decision to make. Basically, it's about a girl named Utena who comes to a private school where the student council members duel each other to possess the Rose Bride, a mysterious girl named Anthy. Which sounds like a pretty weird story, and it is-- but there's a lot more to it than that. It's a really great fantasy take on adolescence and coming of age, with beautiful artwork and storytelling by Saito. There is also an anime series and movie, each of which have a story that's pretty different from the manga. The manga story-line is the best in my opinion, with the movie coming in second and the anime (which is kinda crazy) last.
CLAMP - CLAMP is not a manga but the name of a group of artists (manga-ka) who work together to produce some of the best known titles in the shoujo genre (shoujo is "girl's comics"). Some of their most famous works are: Card Captor Sakura, X, Tsubasa, XXX-holic, Magic Knights Rayearth, etc. The list could go on for a long time. My favorite series by them is Tsubasa Resevoir Chronicle. It's a fantasy about a group of travelers on a quest to find the missing pieces of Princess Sakura's memory, which have been scattered throughout a number of worlds. The plot is fairly complicated, with interesting back stories, and as always the illustration and character designs are absolutely gorgeous. It's a fun series for fans of CLAMP's work, because the worlds visited by the travelers are based on previous series, with many popular characters making a comeback in a new setting.
One more manga by CLAMP that I have to recommend is Shirahime-syo. It's a one-shot manga re-telling of an old Japanese folklore story about a winter spirit who comes to visit a human man. The illustrations are stunning and it's a great introduction to classic Japanese legends.
Battle Angel Alita - by Yukito Kishiro (銃夢 - ganmu) It's a post-apocalyptic sci-fi story about a cyborg girl named Alita who has lost her memory and is trying to put together the pieces of her dark past. The series is extremely violent, but if you're not too squeamish I highly recommend it- it's a fast-paced, exciting story with deeper themes than just gratuitous violence. Definitely one of my favorite series.
Saint Oniisan - by Hikaru Nakamura (聖☆おにいさん) This is not a series I see being translated and sold in the West anytime soon, which is unfortunate because it's very funny and entertaining. The two main characters are Jesus and Buddha, who are best friends/roommates living in modern day Japan. Despite the sacrilegious premise, it's a very light-hearted story which reflects Japan's "live and let live" approach to religion. Aside from being really funny, it's also an interesting look at how a modern eastern culture views Buddhism and Christianity. It hasn't been translated yet as far as I know, but you can read an English scanlation here.
Deathnote - by Takeshi Obata (デスノート). Deathnote is a thriller about a boy who discovers a notebook belonging to a god of death; anyone whose name is written in the notebook will die. I recommended the movie version as well in this post, but I would really suggest reading the manga first. The story is different and the twists and turns will be much more exciting if you start with the comics and then move on to the movie. It became extremely popular in the anime/manga world since its release, thanks to the page-turner story-telling and the memorable characters.
Fushigi Yuugi - by Yuu Watase (ふしぎ遊戯). This was one of the first manga I ever read, back in the days when the "manga" section at my bookstore had only 4 comics on the shelf. I get pretty nostalgic about this series, so even though it is a bit silly it will always hold a place in my heart. It's another fantasy series, about a girl named Miaka from modern day Japan who falls through a book into a world based on ancient china. There she becomes the priestess of the god Suzaku and must go on a quest to find the warriors of Suzaku. It's definitely for a younger audience, but nevertheless it's a cute, entertaining story with some of my favorite characters in the manga world. Some of the more recent spin-offs, like the Genbu Kaiden are better for older readers, with somewhat more mature story-lines.
Yasha - by Akimi Yoshida (夜叉). Yasha is not a very well-known series; it's one of those hidden gems of the manga world. It's a psychological thriller about twins separated at birth, one of whom is a prodigy that becomes a doctor and is researching a deadly virus. The other is raised by their father, a dangerous man involved in crime. The plot is really interesting, with lots of twists and surprises and it always keeps you guessing at the characters' real motivations. The series was turned into a live action drama back in the 90's, although the little I saw of the series didn't seem that great. I definitely recommend the manga version; there's no translation yet, but there's an English scanlation available here. I also recommend Banana Fish, the series Yoshida is most famous for- like Yasha, it's an exciting thriller with many interesting, complicated characters.