I don't have a specific favourite (though I usually say FLCL). I really liked reading Yokohama Kaidashi Kikou (a sci-fi about an android who owns a coffee shop in an idealic, post-apocolyptic rural Japan) and Yotsuba&(a slice of life tale about an irrepressable five year old girl).
As for anime, I haven't especially liked one since seeing Ponyo at the cinema. Anime tends to feel too immature for my tastes now. I actually prefer ones aimed at girls now, like Ouran Highschool club (a gender-bending story set in highschool), or Axis Powers Hetalia (the history of the world, told through characters who embody their national stereotypes).