I don't work with Drupal, but I do work with Joomla a lot. I deploy by archiving all the files in the web root (tar and gzip in my case, but you could use zip) and then uploading and expanding that archive on the production server. I then take a SQL dump (mysqldump -u user -h host -p databasename > dump.sql), upload that, and use the reverse command to insert the data (mysql -u produser -h prodDBserver -p prodDatabase < dump.sql). If you don't have shell access you can upload the files one at a time and write a PHP script to import dump.sql.
