Like everybody... manga folder -> a folder for each series -> folders by chapters or volumes, :P
I also have a folder called "fix later" where I put all the chapters that I can organize yet, oh! I rename each folder :P every chapter is unzipped ^^U
I just burn in a dvd all the anime, I love manga and keep it... and cannot delete it ^^U hurt my heart just to think to delete it XD
The size of the folder is around 20 gb and I'm proud of it!!!