Ideally I would prefer not to have a password for a database in its raw form in a config file.
Is there away that pdo mysql connect accepts a md5 or sha1 version??
The best way it to put restrict access to the server by an IP address like dogmatic69 suggestion. using 127.0.0.1 if the database server is on the same server as the web server or use the IP address of the web server if the database server is on a different server.
1) make the file only accessible to www-data.
2) never use a username/pw combo that has more privelage than needed (eg no grant, drop, create etc, only select insert)
3) make mysql only accept connections from 127.0.0.1
If someone has access to your box you have more problems than worrying about your applications db password.