У каждого свои методы. Я ставлю так:

777

administrator/cache/
administrator/components/
administrator/modules/
administrator/templates/
administrator/language/
administrator/language/en-GB/
administrator/language/ru-RU/
cache/
components/
images/
images/banners/
images/stories/
language/
language/en-GB/
language/ru-RU/
media/
modules/
plugins/
plugins/content/
plugins/search/
plugins/system/
templates/
tmp/
logs/
upload/

644 Остальные папки
444 .htaccess и остальные кроме sitemap.xml