I just updated PHP and MySQl on my VPS with the current Versions from Atomic Repo.
Everything worked out fine so far.
From console I get the new PHP 5.3:
[root@server phpMyAdmin]# php -v
PHP 5.3.16 (cli) (built: Aug 20 2012 11:18:05)
Copyright (c) 1997-2012 The PHP Group
Zend Engine v2.3.0, Copyright (c) 1998-2012 Zend Technologies
with the ionCube PHP Loader v4.0.5, Copyright (c) 2002-2011, by ionCube Ltd.
But through Apache I still get the old version (5.1.6).
The server is running some old version of crappy Plesk Panel. That gives me the option to choose between Apache Modul, fCGI and CGI-BIN.
Any hints, how to update apache, so it will use the new PHP Version?
EDIT: I just needed to restart httpd (/etc/init.d/httpd restart)