The following files are changed from the upstream RPMS.  All changes are trademark and look/feel related unless otherwise noted under the specific RPM.
anaconda
 
Path of the Distribution changed from RedHat to CentOS on the install CDs.
anaconda-help
 
anaconda-product
 
anaconda-runtime
 
apr
 
apr-devel
 
centos-release
 
File name changed from redhat-release in the upstream product.
dhclient
 
dhcp
 
This file had to be compiled on an older version of gcc than ships with CentOS-4 and was modified to accomplish this. See bug#861 at bugs.centos.org
dhcp-devel
 
firefox
 
In addition to numerous shortcut changes, added the CACert.org certificate as a trusted Certificate Authority.  See CentOS.org for details.
firstboot
 
glade2
 
Corrected a race condition.  See bug#855 at bugs.centos.org.
gnome-desktop
 
gnome-desktop-devel
 
gnome-session
 
httpd
 
httpd-devel
 
httpd-manual
 
httpd-suexec
 
indexhtml
 
initscripts
 
libtool
 
libtool-libs
 
libtool and libtool-libs require a rebuild when used with a new version of gcc.
mod_perl
 
mod_perl-devel
 
mod_ssl
 
mozilla
 
In addition to numerous shortcut changes, added the CACert.org certificate as a trusted Certificate Authority.  See CentOS.org for details.
mozilla-chat
 
mozilla-devel
 
mozilla-dom-inspector
 
mozilla-js-debugger
 
mozilla-mail
 
mozilla-nspr
 
mozilla-nspr-devel
 
mozilla-nss
 
mozilla-nss-devel
 
redhat-artwork
 
redhat-logos
 
rhn-applet
 
Modified to not use the RHN and to instead use the CentOS Mirror Network.
squirrelmail
 
up2date
 
Modified to not use the RHN and to instead use the CentOS Mirror Network.
up2date-gnome
 
ypserver
 
ypserver on the install discs was modified to fix a problem that rendered it non-functional, see bug #1253 at bugs.centos.org.
Note:
 The following packages are added to CentOS and are not in the upstream product to allow the use of yum for updates:
createrepo
 
centos-yumconf
 
sqlite
 
sqlite-devel
 
python-elementtree
 
python-sqlite
 
python-urlgrabber
 
yum
 
New Update System:
A new update system for CentOS has been released that issues geographically based, fresh mirrors and provides for mirror failover.  Please see this article on the 
new update system for details.
More Information:
For more Information, see the 
CentOS-4  Documentation at CentOS.org, or the /NOTES directory on CD-1 of this distribution.  The documentation is provided {and copyrighted} by 
Red Hat®,Inc.  The CentOS Project redistributes these original works (in their unmodified form) as a reference for CentOS-4.  CentOS-4 is built from publicly available, open source SRPMs.