I've screwed my CentOS 6 server. I've ran chmod on a few symlinks and changed permissions important file such those in /bin and all commands even clear says Permission Denied. Now It is unable to boot.
How do I restore permissions?
Honestly, boot a live cd and grab a backup of the files you need. Then head to re-install town.... :(
You MIGHT be able to install over your broken version and only break a few [hundred] things...
Sounds like you've overly restricted a bunch of system directories. Before I tell you how to solve your immediate issue you should know that default permissions differ throughout and there's no simple way I can think of to recover this without backup recovery or some level of re-installation. The security and stability of the system may be seriously compromised.