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Please note: Some of these scripts are free and others are not. I am not recommending or endorsing any scripts or saying that they will work on your server.

http://www.zubrag.com/scripts/
http://www.cplicensing.net/scripts.php
http://www.rocketdownload.com/scripts/query.php?q=cpanel (4 Pages)
http://www.findmysoft.com/scripts/search_result.php?word=cpanel&x=0&y=0&search=Search
http://scriptmafia.org/

Here is a complete list of all of the scripts in the /scripts folder from cPanel 11.25.0-E40223 – WHM 11.25.0 – X 3.9
http://twiki.cpanel.net/twiki/bin/view/AllDocumentation/WHMDocs/WHMScripts

This is an older list of scripts that used to be correct. I will try and locate the differences and upload the here in the future.

adddns – Adds a DNS zone.
addfpmail – Add frontpage mail extensions to all domains without them.
addfpmail2 -Add frontpage mail extensions to all domains without them.
addnetmaskips – Add the netmask 255.255.255.0 to all IPs that have no netmask.
addnobodygrp – Adds the group nobody and activates security.
addpop – Add a Pop Account.
addservlets – Add JSP support to an account (requires tomcat).
addstatus – (Internal use never called by user).
adduser – Add a user to the system.
admin – Run WHM Lite.
apachelimits – Add rlimits to Apache
betaexim – Installs the latest version of exim.
biglogcheck – looks for logs nearing 2 gigabytes in size
bsdcryptoinstall – Installs crypto on FreeBSD.
bsdldconfig – Configures the proper lib directories in FreeBSD.
bsdpkgpingtest – Tests the connection speed for downloading FreeBSD packages.
buildbsdexpect – Install expect on FreeBSD.
buildeximconf – Rebuilds exim.conf.
buildpostgrebsd-dev – Installs postgresql on FreeBSD.
checkbadconf – Checks /usr/local/apache/conf/httpd.conf for bad users.
checkbsdgroups – Checks and repairs proftpd ownership on FreeBSD.
checkccompiler – Checks to make sure the C compiler works on your system.
checkfpkey – Checks for the FrontPage suid key
checkgd – Checks to see if GD is built.
checkinterchange – (Internal use).
checklibssl – Checks to make sure the proper libssl symlinks exist.
checkmaxclients – Checks to see if apache has reached the maximum clients allowed.
checkoldperl – Checks to see if the version of Perl on your system is old.
checkrsync – Checks to make sure rsync is up to date.
checksuexecpatch – Checks to see if mailman has been patched for suexec.
checksuspendpages – Checks to see if suspend pages are properly named.
checkup2date – Makes sure up2date is set up properly (RedHat)
checkyum – Makes sure yum is set up properly.
chkpaths – Makes sure /usr/sbin/chown has a symlink to /bin/chown
chownpublichtmls – Change ownership of all users web space to them, which is useful for converting to suexec. Files owned by nobody are deleted.
chpass – Change password.
ckillall – Allows you to kill a process (used like killall).
ckillall2 – Allows you to kill a process.
cleanbw – Cleans up old bandwidth logs.
cleandns8 – Clean up named.conf.
cleangd – Cleans up old GD installs and reinstalls GD
cleanmd5 – Fix CPAN md5 problems.
cleanmsglog – cleans exim’s msglog
cleanupmysqlprivs – Cleans up improper mySQL privileges.
compilers – Disables the usage of compilers for unprivileged users.
convert2maildir – Converts mail from mbox to maildir format and installs courier impap and pop (cpimap is removed).
courierup – Updates/Installs Courier
cpbackup – Runs backups.
distupgrade – Upgrades RedHat to the newest version (for testing only)
dnscluster – Enables DNS clustering.
dnsqueuecron – Adds a cron job to dump the DNS queue.
dnstransfer – Only if the server has a DNS master (sync with DNS master).
downgradefp – Downgrades FrontPage Extensions (to 5.0-0)
dropmysqldb – Drops a mySQL database.
easyapache – Upgrade Apache
editquota – Change a users quota.
enablechkservdwebmail – Enable service checking of webmaild.
enablefileprotect – Protects home directories if file protection is built in apache.
ensurepkg – Installs a FreeBSD package.
ensurerpm – Installs a rpm.
exim3 – Installs exim 3.
exim4 – Installs exim 4.
exim4-rh73test – Installs exim release #260. (RedHat only)
eximcron – Creates a cron job for exim_tidy_db.
eximlocalsend – Enables/Disables exim local sending.
exim_tidydb – Cleans the exim message log.
eximup – Installs/Updates exim.
fetchgd – Includes libg.so.
findhacks – Search for common Trojan Horses.
findoddrootprocesses – Lists root processes that may need to be checked out.
findphpversion – Check to see if your php version file is up to date.
findtrojans – Exhaustive Trojan Horse search.
fixallcartswithsuexec – Fixes permissions on carts when using suexec.
fixallinterchangeperm – Fixes permissions on all users’ Interchange Shopping Carts.
fixbinpath – Makes sure all bin file paths are correct.
fixbuggynamed – Updates bind to solve any problems with bugs.
fixcommonproblems – Attempt to fix the most common problems.
fixetchosts – Fixes problems with /etc/hosts
fixeverything – Fix common problems and quotas.
fixfpwml – Fix for .wml errors with frontpage.
fixheaders – Run if nothing compiles errors with .h files on compile.
fixinterchange – Reinstall interchange Perl modules.
fixinterchangeperm – fix permissions on a user’s interchange cart.
fixipsnm – Same as addnetmask ips, but Perl though.
fixlibnet – Reinstall Bundle::libnet (Perl).
fixlocalhostwithphp – Change /etc/hosts to work better with PHP 4.2.0 + MySQL.
fixmailman – Updates and restarts mailman.
fixmailmanwithsuexec –
fixmuse – Reinstalls muse.
fixmysql – Fixes problems with mySQL.
fixmysqlbsd – Fixes problesm with mySQL on FreeBSD.
fixnamed – Updates bind to handle many DNS zones (more than 512).
fixndc – Repair redhat’s broken named.conf on 7.2.
fixoldlistswithsuexec – Run after enabling suexec on the server to change the URLs that Mailman gives out to ones that don’t give a 500 internal server error.
fixperl – Symlink /usr/local/bin/perl /usr/bin/perl.
fixperlscript – Makes sure a perlscript includes all corresponding modules.
fixpop – Fix a POP account and reset password.
fixproftpdconf – Fixes problems with /usr/local/etc/proftpd.conf
fixproftpddupes – Updates proftpd.
fixquotas – Fix quotas.
fixrndc – Fixes named.conf to prevent rndc staus failed.
fixspamassassinfailedupdate – Reinstalls a failed spamassassin update.
fixsubdomainlogs – Run if subdomain logs don’t show up in cPanel.
fixsuexeccgiscripts – Fix CGI scripts that are broken after suexec installed.
fixvaliases – Fix permisions on valiases.
fixwebalizer – Repair a Webalizer that has stopped updating.
fp3 – Updates the fpexe3 patch.
fpanonuserpatch – Updates FrontPage extensions to include the anonymous user patch.
ftpcheck – Checks for FTPSSL.
ftpquaotacheck – Runs quota checking for all ftp users.
ftpup – Updates your ftp server.
fullhordereset – Resets Horde and displays the current Horde password.
futexfix – Fixes problesm with futex.
futexstartup – Starts futex.
gcc3 – Installs gcc-3.3.3

gencrt – Generate a .crt and .csr file.
grpck – Checks to see if grpck is working properly.
hdparmify – Enable dma/irq/32bit HD access, which speeds up IDE drives.
hdparmon – Turns on hdparm.
initacls – Mounts your file systems with ACL support (make sure your kernel supports ACLs)
initfpsuexec – Enable FrontPage suexec support.
initquotas – Turn on quota support on new drives.
initsslhttpd – Make sure HTTP starts with SSL.
initsuexec – Turn on suexec support if suexec is installed.
installcgipm – Installs CGI.pm
installdbi – Install Bundle::DBD::mysql.
installfpfreebsd – Installs FrontPage 5 Extensions on FreeBSD.
installfpgentoo – Installs FrontPage on Gentoo.
installgd – Builds GD.
installpkg – Installs a FreeBSD package.
installpostgres – Installs PostrgeSQL.
installrpm – Installs a rpm.
installspam – Install SpamAssassin.
installssl – Add a SSL vhost.
installzendopt – Install zend optimzer.
installzendopt-freebsd – Install zend optimizer on a freebsd machine.
isdedicatedip – Checks an ip to see if it is dedicated.
killacct – Delete an account.
killbadrpms – Security script that kills insecure RPMs from the server.
killdns – Delete a DNS zone.
killdrrootvhost – Removes the document root for a virtual host.
killndbm – Remove the broken NDBM_File module from 7.2.
killpvhost – Removes a virtual host from proftpd.conf.
killspamkeys – Removes a spam key.
killsslvhost – Removes a SSL entry for a virtual host.
killvhost – Delete a vhost.
listcheck – Checks mailing lists for issues.
listproblems – Lists common problems.
listsubdomains – List subdomains.
mailperm – Fix almost any mail permission problem.
mailscannerupdate – Updates MailScanner
mailtroubleshoot – Guided mail fix.
makecpphp – Installs php.
makesecondary – Part of DNS transfer.
manualupcp – Updates cPanel manually.
md5crypt – Encrypts a password into MD5.
mseclocal – Sets up Mandrake’s msec to allow exim to run as mailnull.
mysqladduserdb – Create a MySQL databse and user.
mysqlconnectioncheck – Attempts to connect to MySQL, restarts SQL if necessary.
mysqldeluserdb – Delete a MySQL database and user.
mysqlpasswd – Change MySQL password.
mysqlrpmpingtest – Checks your connection speed for downloading mySQL rpms.
mysqlup – Updates mySQL.
ndbmcheck – Checks to see if the nbdm module is loaded (kills in RedHat 7.2)
netftpsslpatch – Patches FTPSSL.pm.
newexim – Installs the latest version of exim.
nofsck – Make fsck always use -y
nomodattach – Removes mod_attach from httpd.conf.
nomodauthmysql -Removes mod_auth_mysql from httpd.conf.
nomodbwprotect – Removes mod_bwportect from httpd.conf.
nomodgzipconfmods – Removes mod_gzip from httpd.conf.
nomodperl – Removes mod_perl from httpd.conf.
oldaddoncgi2xaddon – Updates old addons to X addons.
park – Parks a domain.
patcheximconf – Fixes exim.conf.
perlinstaller – Installs perl.
phpini – Create a php.ini file.
pingtest – Checks your download time from cPanel mirrors.
pkgaccount-ala – backs up an Alab*nza account for transfer.
pkgacct-ciXost – backs up a ci*ost account for transfer.
pkgacct-dXm – backs up a d*m account for transfer.
pkgacct-enXim – backs up an en*im account for transfer.
pkgacct-pXa – backs up a p*a account for transfer.
proftpd128 – Installs proftpd-1.2.8.
ptycheck – Fixes permissoins on /dev/ptmx.
pwck -Verifies the integrity of system authentication information.
quickkernel – Updates your kernel.
quicksecure – Quickly kill useless services.
rebuildcpanelsslcrt – Rebuilds the cPanel SSL Certificate.
rebuildcpusers – Rebuilds /var/cpanel/users.
rebuildetcpasswd – Rebuilds /etc/passwd.
rebuildeximbsd – Rebuilds exim on FreeBSD.
rebuildhttpdconffromproftpd – Rebuild httpd.conf from the proftpd.conf file.
rebuildinterchangecfg – Used after moving a domain with Interchange to the server.
rebuildnamedconf – Restore named.conf from files in /var/named.
rebuildproftpd – Restore proftpd.conf from httpd.conf.
reinstallmailman – Reinstalls mailman.
relocatevartousr – Relocates files from /var to /usr in case of disk space issues.
remdefssl – Remove default SSL vhost.
reseteximtodefaults – Resets exim’s default settings.
resetimappasswds – Resets all imap passwords.
resetquotas – Change quotas to what they should be .
restartsrv – Restart a service.
restartsrv_apache – Restart apache.
restartsrv_bind – Restart bind.
restartsrv_clamd – Restart clamd.
restartsrv_courier – Restart courier imap.
restartsrv_cppop – Restart cppop.
restartsrv_entropychat – Restart entropy chat.
restartsrv_exim – Restart exim.
restartsrv_eximstats – Restart exim statistics.
restartsrv_ftpserver – Restart your ftp server.
restartsrv_httpd – Restart httpd.
restartsrv_imap – Restart impad.
restartsrv_inetd – Restart inetd.
restartsrv_interchange – Restart Interchange Shopping Cart.
restartsrv_melange – Restart melange chat.
restartsrv_mysql – Restart mysqld.
restartsrv_named – Restart named.
restartsrv_postgres – Restart postgresql.
restartsrv_postgresql – Restart postgresql.
restartsrv_proftpd – Restart proftpd.
restartsrv_pureftpd – Restart pure-ftpd.
restartsrv_spamd – Restart spamd.
restartsrv_sshd – Restart sshd.
restartsrv_syslogd – Restart syslogd.
restartsrv_tomcat – Restart tomcat.
restartsrv_xinetd – Restart xinetd.
restoremail – Restores a user’s mail.
reswhostmgr – Restart whostmgr.
rpmup – Upgrade redhat/mandrake errata/security.
rrdtoolinstall – Installs RRD Tool.
runstatsonce – Runs statistics (should be used from the crontab).
runweblogs – Run analog/webalizer/etc. for a user.
safeperlinstaller – Installs perl safely.
safeup2date – Runs up2date safely.
safeyum – Runs yum safely.
secureit – Remove unnecessary suid binaries.
securemysql – Attempts to secure the MySQL configuration.
securetmp – Adds securetmp to system startup.
setupfp – Install FrontPage 3 on an account.
setupfp4 – Install FrontPage 4 (2000) installer on an account.
setupfp5 – Install FrontPage 5 (2002) installer on an account.
setupfp5.nosueuxec – Install FrontPage 5 (2002) installer on an account when not using suexec.
showexelist – Shows exe processes.
simpleps – Display the process list.
smartcheck – Checks hard drive integrity.
smtpmailgdionly – Enables SMTP Mail Protection.
spamboxdisable – Disables SpamAssassin’s spambox delivery for all accounts.
suspendacct – Suspends an account.
sysup – update cPanel RPMs.
unlimitnamed – Installs the latest version of bind patched to support greater than 512 ips on the server.
unblockip – Unblocks an IP blocked by portsentry.
unsetupfp4 – Removes FrontPage 4 or 5 from an account.
unslavenamedconf – If the user accidentally sets a DNS master as local server, this will repair named.conf after the loop.
unsuspendacct – Unsuspends an account.
upcp – Updates cPanel.
updated – Updates /scripts.
updatefrontpage – Updates FrontPage
updatenow – Updates /scripts NOW.
updatephpconf – Updates PHP configuration files.
whoowns –
Finds out who owns a domain.
wwwacct – Creates an account.
xaddonreport – Reports the current addon scripts installed.