Below are the changes needed to be done for your custom php.ini to work with php 5.3 being installed on the servers , we will announce servers upgraded a day before the upgrade so you get prepared, here are the changes :
Change line 
PHP Code:
error_reporting  =  E_ALL & ~E_NOTICE  
PHP Code:
error_reporting = E_ALL & ~E_NOTICE & ~E_DEPRECATED  
Change line 
PHP Code:
post_max_size = 16M  
PHP Code:
post_max_size = 64M  
Change line 
PHP Code:
gpc_order = "GPC"  
PHP Code:
;gpc_order = "GPC"  
PHP Code:
magic_quotes_gpc = On  
PHP Code:
;magic_quotes_gpc = On  
PHP Code:
extension_dir = "/usr/local/lib/php/extensions/no-debug-non-zts-20060613"  
PHP Code:
extension_dir = "/usr/local/lib/php/extensions/no-debug-non-zts-20090626"  
PHP Code:
zend_extension="/usr/local/IonCube/ioncube_loader_lin_5.2.so"  
PHP Code:
zend_extension="/usr/local/ioncube/ioncube_loader_lin_5.3.so"  
PHP Code:
zend_extension="/usr/local/Zend/lib/Optimizer-3.3.9/php-5.2.x/ZendOptimizer.so"  
PHP Code:
zend_extension="/usr/local/Zend/lib/Guard-5.5.0/php-5.3.x/ZendGuardLoader.so"  
PHP Code:
date.timezone="Asia/Jakarta"