@VisioN's answer didn't work that well for me, although it was facing the right direction. I tweaked it a little bit:
var regexp = /[\xAE]/;
$('body :not(script,sup)').contents().filter(function() {
return this.nodeType === 3 && (regexp.test(this.nodeValue));
}).replaceWith(function() {
return this.nodeValue.replace(regexp, '<sup>$&</sup>');
});
This method makes use of the character hex, instead of using the character code. I looked up the hex on character-codes.com and picked the character hex of the ® character. The value is AE
so that's how I got to my solution. Let me know if this one worked for you!