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Upgrade from what? On which distro? How complex are your databases?
We recently upgraded to Apache 2.2, there are some basic modules that have changed (mod_access for example) that required us to modify our apache configuration file. Our databases were mostly simple, very straight forward standard databases, so the move from MySQL 3 to 5 was "no biggie" and the same help true for moving from PHP 4 to PHP 5.
This was on Gentoo based systems using standard portage tools to update.
from apache 1.3 to 2.2, php4 to php5 and mysql 4.3 to mysql 5
and our database wont say they are big just 40G and been backed up
i am think of installing a the newer version of mandriva 2008 instead of only the packages
im currently using redhat 4 ent and debian 3
I would setup a test box, configure it with the new versions of the applications. Copy your databases and site to the new box and test, test, test.. once you work out the kinks it will be easy to upgrade the in-place system..