I'm really just re-wording what @Marshall House says here, but:

In HTML, a double quote (") will always end an attribute, regardless of a backslash - so it sees: onclick="var a = prompt('New value: ', 'aaaa\". The solution that @Marshall offers is to separate your code out into a function. This way you can print escaped PHP into it without a problem.

E.g.:

<script>
    // This is a function, wrapping your code to be called onclick.
    function doOnClickStuff() {
        // You should no longer need to escape your string. E.g.:
        //var a = prompt('new value:','<?php echo i]; ?>');
        // Although the following could be safer
        var a = prompt('new value:',<?php json_encode(i]); ?>);
        if (a) { <!--javascript code--> }
        else { <!--javascript code--> }
    }
</script>
<someelement onclick="doOnClickStuff();"> <!-- this calls the javascript function doOnClickStuff, defined above -->

1. Never echo JS from PHP. Escape from PHP mode instead, it will save you a lot of slashes and nerves.
2. Every value have to be escaped properly, as explained in this article

So, for the JS values you have to escape them with json_encode() and, as they are going into HTML attribute, escape them as HTML too.
For the last element only HTML encoding is required.

foreach ($array as $element) 
{
    $param1 = htmlspecialchars(json_encode($element[0])); // better give them 
    $param2 = htmlspecialchars(json_encode($element[1])); // meaningful names
    $param3 = htmlspecialchars($element[2]);
?>
<a onClick="myFunctionTakesPHPValues(<?=$param1?>,<?=$param2?>)">
   <?=$param3?>
</a>
<? }

And yes, using raw JS in HTML attributes considered as a bad practice.

My other answer explains the general best practice, let's go over your code.

• You can pass an array to str_replace() so that it replaces every occurence of matching substrings with their replacement array counterparts with the same index:

  return str_replace(["/", "\n"], ["\\/", "\\n"], $subject)

• You aren't escaping ; for JavaScript strings, that can be used to break out of the context.

• You shouldn't really care about JavaScript replacement. Data comes from the server, that's where all escaping should be.

• ES5 has the Array.isArray() static method to check if a given parameter is an array. For strings, typeof str will return string. So your getType function is a bit redundant:

  function isString(str) { return typeof str === 'string'; }
  function isArray(arr) { return Array.isArray(arr); }

• Also, ES5 has Array.prototype.forEach for iterating over an array, and is considered a better alternative to for.

encode it with JSON

rawurldecode('%73%6F%6D%65%74%68%69%6E%67');

Due to respects of readability and future maintainability, I'd like to point out a few things which may help you out.

First, I see you're generating HTML elements in a PHP string. This isn't inherently bad, but when your string wraps across 2 or more lines, it becomes increasingly difficult to manage. Instead, you may want to think about escaping PHP for outputting HTML portions, and re-entering PHP for logical portions. You can escape PHP and enter HTML within if statements, function declarations etc, so there's really no good reason not to. Look at the following example (this solution also escapes the strings in an appropriate manner where its value can contain single quotes, double quotes or line breaks):

<?php

function urlFriendly($input) {
    return urlencode($input);
}

function jsFriendly($input, $urlFriendly = True) {
    $output = htmlentities($input, ENT_QUOTES);
    // Double quotes in PHP translate "\n" to a newline.
    // Single quotes in PHP keep the literal value.
    $output = str_replace("\r\n", '\n', $output); // Windows support
    $output = str_replace("\n", '\n', $output); // Linux support
    if($urlFriendly) { // Encode for use in URLs
      $output = urlFriendly($output);
    }
    return $output;
}

$vrj_name = 'vrj';
$messageContent_vrj = 'message content';
$from_email = 'from email';
$email = 'email';
$subject = 'subject line';

?>
<script type="text/javascript">
    function SelectRedirect() {
    switch(document.getElementById('s1').value) {
        case '?vrj_name=<?php print jsFriendly($vrj_name);?>':
            var toloc = '?vrj_name=<?php print jsFriendly($vrj_name);?>';
            toloc    += '&messageContent=<?php print jsFriendly($messageContent_vrj);?>'';
            toloc    += '&from_email=<?php print jsFriendly($from_email);?>';
            toloc    += '&email=<?php print jsFriendly($email);?>';
            toloc    += '&subject=<?php print jsFriendly($subject);?>';
            window.location = toloc;
            break;
    }
</script>