How to escape/strip special characters in the LaTeX document?

The only possibility (AFAIK) to perform harmful operations using LaTeX is to enable the possibility to call external commands using \write18. This only works if you run LaTeX with the --shell-escape or --enable-write18 argument (depending on your distribution).

So as long as you do not run it with one of these arguments you should be safe without the need to filter out any parts.

Besides that, one is still able to write other files using the \newwrite, \openout and \write commands. Having the user create and (over)write files might be unwanted? So you could filter out occurrences of these commands. But keeping blacklists of certain commands is prone to fail since someone with a bad intention can easily hide the actual command by obfusticating the input document.

Edit: Running the LaTeX command using a limited account (ie no writing to non latex/project related directories) in combination with disabling \write18 might be easier and more secure than keeping a blacklist of 'dangerous' commands.

Here's some code to implement the Geoff Reedy answer. I place this code in the public domain.

<?

$test = "Test characters: # $ % & ~ _ ^ \ { }.";
header( "content-type:text/plain" );
print latexSpecialChars( $test );
exit;

function latexSpecialChars( $string )
{
    $map = array( 
            "#"=>"\\#",
            "$"=>"\\$",
            "%"=>"\\%",
            "&"=>"\\&",
            "~"=>"\\~{}",
            "_"=>"\\_",
            "^"=>"\\^{}",
            "\\"=>"\\textbackslash",
            "{"=>"\\{",
            "}"=>"\\}",
    );
    return preg_replace( "/([\^\%~\\\\#\$%&_\{\}])/e", "\$map['$1']", $string );
}