cPanel folders and files

A fresh account may have the following directory structure. I say "may" because due to features enabled or disabled by your web host, some directories may or may not be present. Understand you should/may not edit many of these files. All paths relative from ~/ Bolded entries are directories
Underlined entries are files within those directories. If no files are listed, the directory should be empty.

yourdomain.com is your internet domain
* is any string of numbers or letters that varies from server to server or account to account

.bash_logout
.bash_profile
.bashrc
.contactemail Your contact e-mail address set in cPanel
.lastlogin

.cpaddons - Stores information about cPanel Add-ons for this account

.cpaddons/moderation - Stores information for cPanel Add-on installation requests currently in moderation (pending approval from web host)

.cpanel-datastore Information regarding what access privileges this account has
.cpanel-datastore/sbin_ifconfig_-a
.cpanel-datastore/_usr_bin_perl_-v
.cpanel-datastore/_usr_bin_psql_--version
.cpanel-datastore/_usr_local_apache_bin_httpd_-v
.cpanel-datastore/_usr_sbin_mysqld_--version
.cpanel-datastore/apache_GETDOMAINIP_yourdomain.com
.cpanel-datastore/apache_LISTMULTIPARKED_*
.cpanel-datastore/apache_LISTSUBDOMAINS_*
.cpanel-datastore/ftp_LIST_*
.cpanel-datastore/quota_-v
.cpanel-datastore/reseller_*_*

.trash Items "deleted" (moved to trash) in cPanel File Manager

etc/
etc/.imapv4cp5c File storing IMAP information

mail/ Mail data
mail/new Incoming mail that has not yet been marked as received by IMAP
mail/cur Mail sitting on the server
mail/tmp Temporary directory for mail

public_ftp Files to be accessible via anonymous FTP
public_ftp/incoming Files uploaded via anonymous FTP

public_html Directory accessible VIA Apache Web Server (usually for web pages)
public_html/.htaccess The main .htaccess file for the pages served on this cPanel account over HTTP. If you are wiping this account clean, simply delete all the contents in this file.
public_html/cgi-bin Your typical CGI Bin directory, not much to say here.
public_html/images Directory for any images that may be used in your web host's skeleton files (basically pages that are displayed when you haven't set up your website yet, account is suspended etc.). May also be used as a repository for images for any pages you upload.

tmp Temporary files created by cPanel in various activities. Third party scripts may (but rarely) use this directory for their own temporary files.
tmp/analog Temporary files for generation of Analog stats for your website(s)
tmp/awstats Temporary and configuration files for generation of AWStats for your website(s)
tmp/awstats/awstats.yourdomain.com.conf Configuration file for generation of AWStats for a website
tmp/cpbandwidth Temporary directory for tracking bandwidth usage through cPanel
tmp/cpbandwidth/yourdomain.com-bytes_log Number of bytes tranferred by yourdomain.com
tmp/webalizer Temporary files for generation of Webalizer HTTP stats for your website(s)
tmp/webalizer/__db.dns_cache.db Caching of DNS resolution to provide stats based on domain names rather than IP addresses
tmp/webalizerftp Temporary files for generation of Webalizer FTP stats for your website(s)

www Merely points to the public_html directory. If you are performing a backup, remember to exclude this directory as most software does not automatically detect that www and public_html are identical.

The following directories are for use by FrontPage and are present if FrontPage extensions are or have ever been enabled for an account (consult FrontPage documentation for further details):

public_html/postinfo.html Information regarding how to use Microsoft's Web Publishing Wizard with this cPanel account.
public_html/_vti_inf.html Configuration information that FrontPage needs to communicate with the FrontPage extensions on this cPanel account.
public_html/_private
public_html/_private
public_html/_vti_bin
public_html/_vti_bin/.htaccess
public_html/_vti_bin/_vti_adm
public_html/_vti_bin/_vti_adm/.htaccess
public_html/_vti_bin/_vti_aut
public_html/_vti_bin/_vti_aut/.htaccess
public_html/_vti_cnf
public_html/_vti_cnf/.htaccess
public_html/_vti_log
public_html/_vti_log/.htaccess
public_html/_vti_pvt
public_html/_vti_pvt/.htaccess
public_html/_vti_pvt/.roles
public_html/_vti_pvt/access.cnf
public_html/_vti_pvt/botinfs.cnf
public_html/_vti_pvt/bots.cnf
public_html/_vti_pvt/deptodoc.btr
public_html/_vti_pvt/doctodep.btr
public_html/_vti_pvt/frontpg.lck
public_html/_vti_pvt/service.cnf
public_html/_vti_pvt/service.grp
public_html/_vti_pvt/service.lck
public_html/_vti_pvt/service.pwd
public_html/_vti_pvt/services.cnf
public_html/_vti_pvt/svcacl.cnf
public_html/_vti_pvt/writeto.cnf
public_html/_vti_txt
public_html/_vti_txt/.htaccess