Joe,
if you're using mvc, it'll be no problem (jQuery partialview updates etc, etc). however, as you haven't tagged as such i'm presuming webforms (oh, i see the asp.net mvc tag is there now - however, i'll leave the reply as i wrote it at the time as it may be of interest). the good news is, all is not lost and there are in fact page methods that can be used in webforms to stunning effect. i did a quick google and this article seems to nail what i was thinking about:
http://encosia.com/2008/05/29/using-jquery-to-directly-call-aspnet-ajax-page-methods/
i can't comment on the technique too much as i'm definately more in the mvc camp these days, but this is how i'd have done it had i been still heavily using webforms.
jim
[edit] - as the mvc tag is now present, that changes my answer above (or at least means that i should add a little re mvc). what you could do on the masterpage is to ensure that your content pages were ALL partialviews and that your menus invoked a partial refresh. the masterpage would have a 'content' div that you'd update via each jquery menu request. in effect only the inner section of the page would ever change. i know you'd said 'little' change, but depending on the width of your pages, this suggestion could be fairly simple or complex depending on your viewmodels etc. i'll be interested to see further comments.
also, take a look at this (oldish) jeff palermo article re partials and different masterpages: http://jeffreypalermo.com/blog/asp-net-mvc-and-the-templated-partial-view-death-to-ascx/