Pluto is my absolute favorite manga now and forever. Knowing Naoki Urasawa, though, I'll probably read something else of his that piques my interest, but... c'mon. It's a meeting of minds between the genius behind Monster and the defining work of the God of Manga.
A tie between Death Note and Bleach for me. I loved how dark Death Note could be at time, but it also had it's funny moments. I remember reading the whole series in just a week back when it was popular and I even made a Death Note of my own lol. Bleach has some amazing swordfights but the story lacks a certain je ne sais quoi, especially right now when everything seems to be all laggy again even though the author claimed the arc would end around June. Hopefully it gets better, I love it and it has the potential to be even better.
The characters... the adventures... the plot twists... the well thought out plot lines, bringing up things faaaaar from the past... the color spreads... the volume covers... the side cover story chapter story thingies... yeeaaaaaaahhh...
Ew at all of the Bleach and Naruto. One Piece is the only decent member of the Big Three. Naruto's dragging like a snail, and Bleach has no idea where the hell it's going. One Piece is an example of how to do a long runner without causing it to drag.
Anyway, my favorite manga is Fullmetal Alchemist. I also enjoy Shiki, Death Note, D.Gray-man, and Umineko.
It's a tie between Naruto and Katekyo Hitman Reborn. Naruto mostly out of obligation since it was one of my first mangas and KHR because it has awesome characters with a well thought out plot and amazing battles.