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What user does apache run from? What user does php run from? How are they configured to interact with each other? What priveleges do their users have? Are you sure that no executable/script can be uploaded and executed on your server?
Some hardening - / mounted with 'ro' and separate partition with 'rw', directories with no executables with noexec. But that's for true jedies.
Are you aware of current security issues? Like hash function problem in parsing request