Recently we struggled with a difficult issue in WordPress Multisite. We take care of a network of sports weblogs. Each is for a different sport and not all the domain names sound the same.
We have a master install at say worldrecords.org (sample name, not our client's site). Logins only are SSL and all take place at worldrecords.org. An account at any site gets you access to all the sites. Hence login and password takes place at the master domain. Most visitors are not even aware of the domain switch during login.
When people would lose their password, the password reset email would not come from skatinggolds.org or lugegolds.org but from worldrecords.org. Many people would not recognise the domain and would delete the email without clicking and finishing the password reset. Worse yet the email might be considered spam by spam filters.