Most efficient way to write Combination and Permutation calculator in Javascript

Well, here we go!

First of all, why would you ever need to write this?

Math.divide = function(a,b)
{
    return a/b;
}

I would do away with it completely.

You can also clean up your Math.factorial a little bit:

Math.factorial = function(n)
{
    n = Number(n);

    if (isNAN(n)) {
        alert("Factorial requires a numeric argument.");
        return null;
    } else if (n < 2) {
        return 1;
    } else {
        return (n * Math.factorial(n - 1));
    }
}

But the main problem is your onclick() code:

onclick="var n = T1.value; var r = T2.value; var n_minus_r = parseFloat(n) - parseFloat(r); var numerator = Math.factorial(T1.value); var n_minus_r_fact = Math.factorial(n_minus_r); var r_fact = Math.factorial(r); var denominator = n_minus_r_fact * r_fact; T3.value = Math.divide(numerator,denominator); return true;

This is way too complicated. I'd make it a function and bind it to the element, which would get rid of all of the crap in your HTML and make it a bit easier to work with:

window.onload = function()
{
    document.getElementById('calculate').onclick = function() {
        var n = T1.value,
            r = T2.value;

        T3.value = Math.factorial(n) / (Math.factorial(r) * Math.factorial(n - r));
    }
}

And just get rid of the onclick= code.

If you're concerned about efficiency, you'd probably want to re-implement the factorial as an iterative function rather than a recursive one. The recursive version will use a lot more memory and CPU time than the iterative version.

function factorial(n) { 
  var x=1; 
  var f=1;
  while (x<=n) {
    f*=x; x++;
  }
    return f;
}

You also shouldn't be adding your own functions to the Math namespace. It's not a good habit to get into.