Hi,
in IE8 you have the new developer toolbar integrated with which you can profile your javascript. The same can be done with firebug (a free extension to firefox). Profile it and take a look which functions get called the most, then optimize.
C#, in ASP.NET, runs on the server while your javascript runs in the browser. IE6 is known to be leaky on that part and quite slow. Most modern browsers are made with javascript performance in mind (thanks to ajax usage). So you could indeed see a performance gain when you do the calculations on the server and get the output of it via a webservice call via ajax.
But still you can first try to optimize your javascript.
Grz, Kris.