My favorite manga has to be Gakuen Alice. The characters are just lovely! And the plot is great. The only thing that I dislike about it is the fact that too many great characters die...
Here is my top 5 manga list:
3.Mermaid Melody-Pichi Pichi Pitch-
5.Full Moon wo Saga....e
I never managed to actually read the whole FMA manga so I really can't classify it here but I couldn't even compare it with anything(I mean it's shounen manga, right!? All the other ones in my top are shoujo
* Special: Fullmetal Alchemist