RorrKonn, Hayao Miyazaki and Studio Ghibli paint all of their animation cels by hand. 

http://en.m.wikipedia.org/wiki/Hayao_Miyazaki

Hayao hand draws all of the storyboards that the animation team works from. Perhaps the exception, but Miyazaki-San is arguably the greatest living animator.

Check out some of his manga work (hand drawn), from Nausicca of the Valley of the Wind... (Nausicca of the Valley of the Wind manga english: image results).