After a couple years working with different structures I recently found a structure that hols most variations for me:
/project_name (everything goes here)
/web (htdocs)
/img
/css
/app (usually some framework or sensitive code)
/lib (externa libs)
/vendor_1
/vendor_2
/tmp
/cache
/sql (sql scripts usually with maybe diagrams)
/scripts
/doc (usually an empty directory)