Generally, the Server URL and the Notification URL should not be modified. Both these values are TFS-system-wide. So, if multiple application-tiers exist, modifying either one of these values will impact them on all application-tiers

The Notification URL is the URL used in e-mail alerts. This should only change if

1. The name of the computer changes
2. TFS is installed behind a network load balancer. (In which case, the Notification URL should be the front end of the load balancer.)
3. TFS is only accessible via SSL. (In which case, the Notification URL should be the fully-qualified-domain name)
4. People external to the Notification URL's default value, http://computername:8080, in which case the Notification URL should be adjusted accordingly.

The Server URL is the URL TFS uses for communicating with itself. This should only be changed if

1. TFS is only accessible via SSL. (In which case, the Server URL should be the fully-qualified-domain name)
2. Localhost is disabled on the computer hosting TFS. (In which case, the  Server URL should be http://computername:8080)