Since my first impact with the electrical zero and one processing machine, i am thinking about a well structured folder structure - so the same thing you are doing day in and day out ;-). Finally, after many tests, my current folder structure is stable for a long time. This could either mean "it fits my needs" or "well i'm getting used to it". I'm crossing fingers it's the first guess :-). Nevertheless, since this is my blog about coding, politics and the world, i would share my knowledge, so also my folder structure. Take a look to it, i listed the main idea below and also prepared a kind of "folder structure template" you can download. If you have suggestions for improvements, add a comment.
/home/$user |-/backup contains backups |-/bin contains binaries like games, programms |-/code contains sourcecode ____|-/php contains php sourcecode ________|-/script contains php sourcecode ________|-/project contains php projects ________|-/library contains php librarys ____|-/sh contains shellscript sourcecode |-/config contains configuration files ____|-/apache contains apache config files ____|-/bashrc |-/data contains binary user data files |-/doc contains documents ____|-/city contains city relevant files ____|-/financial contains financial files ________|-/2012 contains files from 2011 ____|-/howto contains howtos ____|-/template contains templates, like folder structure template ;-) |-/media contains media ____|-/audio contains audio files ____|-/image contains image files ____|-/video contains video files |-/other contains not sortable files |-/share contains shared files and mounted shares ____|-/out contains provided shares ____|-/in contains mounted shares |-/temp contains temporary files or "to sort" files |-/tool contains toolshome.template.tar.gz