Google Analytics cross domain tracking allows tracking of multiple domains (or sub-domains) in a single Analtics profile. There are loads of great resources for how to implement this, including in unusual client side navigation.
I have come across an issue when using ASP.Net Webforms, where there is a single form for the page and multiple submit actions (server side button onclicks etc) and when we also need a simple form to submit to a different domain. It then becomes more complex to call the relevant client side Google Analytics methods.