I posted this over at AOD (it's really sad how much of a forum/message board hog I am). But since I like making lists I thought I would post this here as well.
I could never make a top favorite list with anime because there are just too many (except Mushi-shi is my number 1) but since I've read less manga it's a bit easier for me
My Number 1
Fullmetal Alchemist
No surprise here I am sure. It's been my favorite manga series for close to 5 years now. It's an adventure story with a very unique developed world with an interesting magic system and history. The characters are all amazing. I can't think of another series with such a large cast where I literally adore every character. In fact even the minor characters have a story to tell. It's tons of fun to read with a great mixture of comedy and drama with a whole lot of heart.
The Rest in no Particular Order (actually in Alphabetical Order)
Fruits Basket
This was my first shoujo series so for that it has a special place to me. I love how it mixes cuteness with somewhat dark undertones. In the end perhaps I did think one too many characters were paired up together but in general it has a great cast of characters and it definitely gives you a very warm feeling from reading.
Hikaru no Go
I just love how you watch the main character grow from a young boy who could care less about Go to a young adult who becomes a very capable professional. Although the story deals with the supernatural aspect of a ghost possessing the main protagonist what I really love about the series is how slice of life and realistic it all felt.
Maison Ikkoku
My favorite Takahashi series: I love how it dealt with more adult issues falling in love, getting over a lost love, graduating from university, getting a job, etc. It's like the perfect slice of life series.
Mushi-shi
Deals with a wanderer named Ginko who travels ancient Japan (probably around the Edo period) helping people deal with supernatural beings called Mushi. Although in many ways I also see the Mushi as a representation of nature. What I love about Mushishi is just how imaginative the series is that it really feels like you are reading a folk tale. The stories also are not just about the mushi but very much about human beings struggles to just live their life and whether the ending is sad or happy usually depends on these human characters' own convictions.
Nodame Cantabile
The story of two university students trying to become professional classical musicians. On the side it is also a romantic comedy between a very crazy girl named Nodame and a somewhat uptight guy named Chiaki. Besides the classical music aspect which I love I also adore the relationship of Chiaki & Nodame. It reminds me of an old Screwball Comedy from the 30's or an I Love Lucy episode. But what makes Nodame Cantable different from those classic comedies is the relationship and their musical careers develop realistically so it doesn't just feel like an endless sitcom.
One Piece
One of those stories where you care more about the journey than the destination. One Piece is a super long series but I don't care because I have so much fun reading it. It's just a silly adventure story with a great cast of unique characters. Still for all the wackiness that are within its pages One Piece can also make my cry like no other series.
Rurouni Kenshin
In general just a fun series with a fun cast of characters. I also liked how the story sort of romanticized the last era of the swords because for me sword fighting was always more cool than gun fights. Finally Kenshin as a character with a dark past was an interesting protagonist and quite different from many shounen heroes. This series also encouraged me to learn on my own more about the Meiji era, the Bakumatsu, Shinsengumi, etc.
Yotsubato!
An extremely charming piece of work and what I recommend if anyone needs a good picker upper. It doesn't really have a plot it just deals with the misadventures of one adorable 5 year old as she interacts with her neighbors, makes discoveries, and just acts absolutely adorable. I am so happy Yen Press will be releasing it again.
Although I only have Maison Ikkoku in my top favorites I do want to make special mention of Rumiko Takahashi since reading her manga (specifically Inuyasha & Ranma 1/2) is a big reason I got into manga in the first place. I was also once obsessed with Inuyasha (and yes my name does come from that but now I keep it because I identify with it despite Inuyasha). Anyways even though that obsession died long ago and I think the series went on way too long I still always enjoyed it to an extent. I just can't stand Naraku and how he would never die.
I also really enjoyed her shorter series One Pound Gospel and Mermaid Saga and I love her short story Fire Tripper (if people think Inuyasha went on too long then I recommend this for what Inuyasha could have been) . Unfortunately though I have not really been keeping up with her new series but starting a new weekly series that could go on for years is a bit daunting for me. One Piece is now like the exception.
Of course I would be interested in hearing what other people's favorites are or if we share any favorites and so forth. :)