While the other answers here will stop the errors being written to your error log, they are simply ignoring the the error message and not fixing the error.
The error in this case is that your php.ini still has either
magic_quotes_gpc on or
magic_quotes_gpc off somewhere in it. The same is true for
register_globals on or
The error is not that the directive is on or off. The error is that the directive shouldn't exist at all. Comment those lines out of your php.ini or remove them entirely and PHP will stop writing errors about deprecated directives.
Of course, this may cause problems with your application if it requires either of those to be on.
The reason this is an error in PHP 5.3 is that in PHP 6, these directives won't even exist and PHP 6 will behave as if they were set to off. If you ever plan on upgrading to PHP 6, now is a good time to start upgrading or replacing your application.
Another solution you could try is downgrading PHP back to the 5.2 or 5.1 branch.
As for PHP writing errors into Apache's log, this is natural because PHP is running as an Apache module. You can put something like
error_log = /var/log/php_errors.log into your php.ini and restart Apache to have the PHP errors separated from your Apache errors. While you're in there, I would recommend changing
off. Error messages can often contain sensitive information that you wouldn't want an attacker to see. You will most likely see this written in your php.ini:
; - display_errors = Off [Security]
; With this directive set to off, errors that occur during the execution of
; scripts will no longer be displayed as a part of the script output, and thus,
; will no longer be exposed to remote users. With some errors, the error message
; content may expose information about your script, web server, or database
; server that may be exploitable for hacking. Production sites should have this
; directive set to off.
There is no sane reason why the error messages contain HTML.
To answer another question that you didn't ask, the reason PHP reports this as being
in <b>Unknown</b> on line <b>0</b> is that the error message was designed for lines of PHP code that you have written but the error it found was in parsing the php.ini before it has even read a single line of code or even opened a .php file. Since it hasn't opened a file and doesn't have a line number, it reports them as "Unknown" and "0".