/etc/

        passwd
        shadow
        group
        exim.conf
        exim.pl
        system_filter.exim
        exim.cert (exim 4)
        exim.key (exim 4)
        proftpd.conf
        proftpd.vhosts.conf
        proftpd.passwd
        hosts
        resolv.conf
        named.conf (/etc/namedb/named.conf on FreeBSD, /etc/bind/named.conf on debian)
        dovecot.conf
        ssh/sshd_config
        virtual/

            domainowners
            domains
            pophosts
            majordomo/*
            *

        httpd/

            conf/

                httpd.conf
                ips.conf
                ssl.crt/

                    server.crt 

                ssl.key/

                    server.key 

            extra/ 

    /var/

        named/* (/etc/namedb/* on freebsd, /etc/bind/* on debian)
        spool/

            virtual/*
            mail/*
            cron/*

        www/*
        log/*
        lib/

            mysql/* (/home/mysql/* on freebsd and debian) 

    /usr/local/

        frontpage/

            *.cnf 

        directadmin/* 

    /home/* 

*Note: these files/directories are what DirectAdmin uses. Do not blindly delete them if you are attempting to uninstall DirectAdmin. Many are required by the system. Deleteing system files can destroy your system.

To reset the permissions on these files, check