Server Information:

CentOS release 4.8 (Final)
PHP Version 4.3.9
mysql Ver 14.7 Distrib 4.1.22

Hope the above helps, basically I'm pretty new to linux and took over looking after a CentOS webserver in June with no prior knowledge of using a UNIX based system. As I have been learning more about Linux I have noticed that the updates just haven't been happening since April last year. Upon further investigation I found the boot partition to be full of old kernels dating back to October 2006. The guy who worked here before was supposed to be a Linux guru :s but seems to have left the system for months with no updates.

My question is: Can I use yum to update mysql and php or should I manually update due to the time in which it hasn't been updated? Also will this affect any web sites hosted on the server? I know I can restart apache gracefully to pick up the changes but I don't want the installers to do so.

Any help would be most appreciated.

You can and should use yum (or up2date) to update mysql and php. You're running CentOS for stability and security patches which RedHat provides. I believe the installer will restart mysql, so you tell us if any web sites will be affected.

You may find this useful http://kbase.redhat.com/faq/docs/DOC-2531. For RHEL/Centos 4.x use the up2date cmds. Keep in mind that since you've done no updates for so long, you'll likely get a new kernel, which will require a reboot.
I'd also recommend some serious backups just in case, before you start.