Partitions:

/
/usr
/tmp
/var
/var/www
/home
/home/desktop

I keep my personal files in:

~/Multimedia/<media type>
~/Texte (text files)

working folders

~/Desktop/Planung (planned stuff)
~/Desktop/Arbeit (stuff I'm working on)
~/Desktop/Fertig (finished things)

each working folder has subfolders like text, coding, taxes, pictures, scripts, php, japanese, laTex and several others.