Because it recently ended, I can say for sure that Hourou Musuko is my favorite manga. I started reading it while I was in my early teens, and I could relate so hard to the protagonist, who yearns to be a female. I can't really explain why I love it so much, but the series was basically just as real as it can get. The pacing was perfect, as if I was living alongside the characters, feeling all of their emotions. The art was really cute, and it inspired the way I draw. The way I see it, I feel as if I actually grew up with the series, going through all the dilemmas the characters did in the manga.
I was going to list Berserk as my favorite, but seeing as that I might die before it actually finishes, I'm not getting my hopes up.