In Gentoo Linux from PHP 5.2 and onwards quite a few things have changed. It is now possible to have a slotted installation of PHP to help people to upgrade to PHP 5.3 and larger. I won’t take the time to explain everything because the Gentoo Dev’s have made a great attempt in creating the PHP Admin Guide. Please read this guide before you attempt the upgrade. Unless you server is a non production system and you don’t care about downtime:

Gentoo Upgrading PHP