Here you go, sir. I refactored it a bit to use an inner loop instead of a buffer array, since it got a bit messy with the additional buffering condition.
// transform carets, e.g. x^2 to x<sup>2</sup> and x^(2y) to x<sup>2y</sup>
function superify(input) {
if(!input) return input;
var output = [];
var alphanumeric = /^[a-z0-9]+$/i;
var i = 0;
var parens;
//outer loop for iterating string
while(i < input.length) {
var current = input[i++];
var next = input[i];
if(current === '^' && next && ((parens = (next === '(')) || next.match(alphanumeric))) {
var first = next;
//start super
output.push('<sup>');
if(!parens)
output.push(first);
//push chars to output until break or string end
while(i++ < input.length) {
current = input[i];
if(parens && current === ')')
break;
if(!parens && !current.match(alphanumeric))
break;
output.push(current);
}
output.push('</sup>');
if(!parens)
output.push(current);
i++;
}
else {
output.push(current);
}
}
return output.join('');
}