So I am just starting to use RHEL/CentOS 5 on newer servers and starting to find some of things that were changed. Normally (in versions 3 or 4) the SSL certificate files were stored in /etc/httpd/conf/ssl.key, etc. Now when you install mod_ssl to enable the https server, the default location for these certificates is in /etc/pki/tls/ (certs & private). It makes sense to move it to a more central location so that it is common with other TLS/SSL oriented services.
I have also just upgraded a server to 5.1 and everything seems to be running well!