Hi KB.
Have you accidentally updated to php 5.4? That would probably explain things. If so:
If you want to keep 5.4, then:
1) PHP Fatal error: Directive 'safe_mode' is no longer available in PHP in Unknown on line 0
For this you need to remove safe_mode line from php.ini (and any sites that have custom php.ini)
One way to think about doing this would be to copy any new php.ini.rpmnew over php.ini but do make a copy of the old one in case there were some customisations you want to keep
2) Failed loading /usr/lib64/php/ioncube/ioncube_loader_lin_5.2.so:
This *could* be indicating that you have an older version of ioncube_loader that is incompatible for 5.4. Fix number 1 first and if you still have the same problem then the solution in this case is to update your ioncube_loader. There are a couple of options here. Scott has an rpm in the atomic repo but you know what? I'd have expected it to have been updated at the same time as php if you got your php 5.4 from atomic (and if the problem really is that you have accidentally upgraded to 5.4). But if it was manually installed then you just need to get the latest version and manually install that in the same way you did it originally.
Please see this
http://www.atomicorp.com/forum/viewtopic.php?f=2&t=7037 for instructions on downgrading for 5.3 if you have accidentally upgraded to 5.4.