You may also want to check out some of important Logs and Paths.

We will provide you an in depth look at all of the fancy scripts cPanel has provided in the /scripts folder. More detailed information to come, so check back soon.

Below are a few examples a just a few scripts:
/scripts/setupfp5 maindomainnameonly.com - Installs FrontPage Extentions
( http://faq.cpanel.net/fp )
/scripts/unsetupfp4 maindomainonly.com - Unsinstsalls Extentions
( http://faq.cpanel.net/fp )
/scripts/runweblogs username - updates stats for user only
/scripts/runlogsnow - activates starts cpanellogd process and starts stats stat log
/scripts/updateuserdomains - This will determin if there is any conflicting domain names located in the:
/var/cpanel/users folders files.
/scripts/adddns -Add a Dns Entry
/scripts/addfpmail -Install Frontpage Mail Exts
/scripts/addservlets -Add JavaServlets to an account (jsp plugin required)
/scripts/adduser -Add a User
/scripts/admin -Run WHM Lite
/scripts/apachelimits -Add Rlimits (cpu and mem limits) to apache.
/scripts/dnstransfer -Resync with a master DNS Server
/scripts/editquota -Edit A User’s Quota
/scripts/finddev -Search For Trojans in /dev
/scripts/findtrojans -Locate Trojan Horses
Suggest Usage
/scripts/findtrojans > /var/log/trojans
/scripts/fixtrojans /var/log/trojans
/scripts/fixcartwithsuexec -Make Interchange work with suexec
/scripts/fixinterchange -Fix Most Problems with Interchange
/scripts/fixtrojans -Run on a trojans horse file created by findtrojans to remove them
/scripts/fixwebalizer -Run this if a user’s stats stop working
/scripts/fixvaliases -Fix a broken valias file
/scripts/hdparamify -Turn on DMA and 32bit IDE hard drive access (once per boot)
/scripts/initquotas -Re-scan quotas. Usually fixes Disk space display problems
/scripts/initsuexec -Turn on SUEXEC (probably a bad idea)
/scripts/installzendopt -Fetch + Install Zend Optimizer
/scripts/ipusage -Display Ipusage Report
/scripts/killacct -Terminate an Account
/scripts/killbadrpms -Delete “Security Problem Infested RPMS”
/scripts/mailperm -Fix Various Mail Permission Problems
/scripts/mailtroubleshoot -Attempt to Troubleshoot a Mail Problem
/scripts/mysqlpasswd -Change a Mysql Password
/scripts/quicksecure -Kill Potential Security Problem Services
/scripts/rebuildippool -Rebuild Ip Address Pool
/scripts/remdefssl -Delete Nasty SSL entry in apache default httpd.conf
/scripts/restartsrv -Restart a Service (valid services: httpd,proftpd,exim,sshd,cppop,bind,mysql)
/scripts/rpmup -Syncup Security Updates from RedHat/Mandrake
/scripts/runlogsnow -Force a webalizer/analog update.
/scripts/secureit -Remove non-important suid binaries
/scripts/setupfp4 -Install Frontpage 4+ on an account.
/scripts/simpleps -Return a Simple process list. Useful for finding where cgi scripts are running from.
/scripts/suspendacct -Suspend an account
/scripts/sysup -Syncup Cpanel RPM Updates
/scripts/ulimitnamed -RH 6 only. Install a version of bind to handle many many zones.
/scripts/unblockip -Unblock an IP
/scripts/unsuspendacct -UnSuspend an account
/scripts/upcp -Update Cpanel
/scripts/updatenow -Update /scripts
/scripts/wwwacct -Create a New Account
/etc/init.d/cpanel restart - Restart cPanel