This is just a short example how I use the Linux file system. A full discussion with lot’s of links you will find on Wikipedia. The home of the Linux File System Hierarchy is here. The layout below is the (almost) default of Debian and Ubuntu distributions.
/home
Just for personal settings, annotations and workspaces.
/tmp
Classic place to put everything short living. Probably best to (automatically) clean it out regularly.
/var/www
Static and dynamic websites
/var/database
Database data-files, if big put on its own logical volume.
/var/<app-name>
Any other non-web, non-db data or archive files.
Other distributions use slightly different file system layouts and the data-files are maybe in different folders, but as mentioned earlier this is my personal approach.