I've deliberated this subject many times before because of my ever-changing manga tastes, but I do believe that I've come to a sound conclusion. Fullmetal Alchemist is my favorite manga series. It wins in character, story, and comedy departments out of all of the series I have read. I like how the story comes around full-circle, and nothing is an asspull. The things that are going on now have been set up since Volume 1, and it is extremely well-planned. Eight years of consistant storyboarding is extraordinary, and that's just the beginning. The steampunk military dictatorship setting is very original (or it was original before a bunch of series started copying it... ahem), and the characters are very solid and likeable. Their personalities are consistant and they go through amazing character development throughout the series. The most developed character is definitely Roy Mustang, who goes through a lot in this series and goes through many changes.
The comedy is pure gold, though it does take away from the seriousness in some scenes. I prefer the comedy when it's used in slow, character-based arcs like in Volumes 5 and 6. The art is a rare breed; it's well-suited for both comedy and action, and I am always amazed by it. Arakawa gives a lot of attention to small details in her art, which is always stunning.
Fullmetal Alchemist is one of the best series out there. It deserves every bit of recognition it gets, unlike a lot of the other top shonen manga.
