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 register_globals off.
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 display_errors to 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".
Best Answer
After the discussion, this sounds like you may have the wrong version of LAMPStack (maybe the 64 bit version instead of the 32 bit version) or possibly a different version of some library that LAMPStack was built against or maybe you have just discovered a bug in LAMPStack. It will be difficult to tell exactly what it is via a Q&A site such as this.
Judging by the name on the download page "LAMPStack 5.4.0-0 dev" it looks like this is the development version of LAMPStack. This generally means that it may have bugs in it and should not be used in production. It is probably also not good for a development machine as you usually want that to be quite similar to your production setup. Their blog post announcing the new version mentions this. They also suggest using their forum to ask any questions you have about it and that is where I would suggest you take these SegFaults now if you plan to continue using the new version.
If you just want to get back to developing your app, I would suggest downgrading back to LAMPStack 5.3.10-1.