Cleaning up deprecated options in php.ini. Add this file in the root directory and call it from a browser. This script does the rest.

gistfile1.php

<?php

class PHP_Ini_Fixes {
	private $deprecated_options = array(
		// Can result in issue in different PHP versions
		'browscap',
		//PHP 5.4 removed
		'register_globals', 'register_long_arrays',
		'magic_quotes_gpc', 'magic_quotes_runtime', 'magic_quotes_sybase',
		'allow_call_time_pass_reference',
		'mbstring.script_encoding',
		'safe_mode', 'safe_mode_gid', 'safe_mode_include_dir', 'safe_mode_exec_dir',
		'safe_mode_allowed_env_vars', 'safe_mode_protected_env_vars',
	);

	private $fixed_files = array();

	public function __construct( $dir ) {
		if ( ! $dir ) {
			$dir = dirname( __FILE__ );
		}

		$this->crawl_dir( $dir . '/' );
	}

	public function show_fixed_files() {
		if ( ! $this->fixed_files ) {
			echo '<p>All files are already fixed. You are ready to go to use the latest PHP version.</p>';
		}
		else {
			echo '<ul>';

			foreach( $this->fixed_files as $file ) {
				echo '<li>' . $file . '</li>';
			}

			echo '</ul>';
		}
	}

	private function crawl_dir( $dir ) {
		$opendir = opendir( $dir ); 		

		while ( false !== ( $file = readdir( $opendir ) ) ) {
			if ( '.' == $file || '..' == $file ) {
				continue;
			}

			if ( is_dir( $dir . $file ) ) {
				$this->crawl_dir( $dir . $file . '/' );
			}

			if ( 'php.ini' == $file ) {
				$this->fix_php_ini_file( $dir . $file );
			}
		}

		closedir( $opendir );
	}

	private function fix_php_ini_file( $file ) {
		$changed       = false;
		$content       = file_get_contents( $file );
		$content_parts = explode( PHP_EOL, $content );

		foreach ( $content_parts as $key => $part ) {
			$needle = strtok( $part, ' ' );

			if ( in_array( $needle, $this->deprecated_options ) ) {
				$changed = true;
				unset( $content_parts[ $key ] );
			}
		}

		$content = implode( PHP_EOL, $content_parts );

		if ( $changed ) {
			$this->fixed_files[] = $file;

			file_put_contents( $file, $content );
		}
	}

}

echo '<h1>php.ini file fixed</h1>';

$fixer = new PHP_Ini_Fixes(false);
$fixer->show_fixed_files();