Recently, I have been studying the inner work of Service Applications in SharePoint 2010.
I have discovered several terms that can be confusing if you haven't dived yet into the theory.
Service application - in the general case, are just a logical concept made up of one or more components, one of which may be an actual Service Application component that defines the configurations for a particular implementation of a specific Service Instance." (Gary Lapointe's book)
Service application (second meaning - most used) - a management interface with some SQL back end (_admin/ServiceApplications.aspx)
Service application Endpoint - IIS Virtual application - a WCF service (a WCF service per a service application)
Service instance - a dll, register keys, binary files, timer job (_admin/Server.aspx)
(Got Access denied error on _admin/Server.aspx? - Read on Simple concept: Manage services on server link is missing)
Here is a simple picture to see the relationships between the components of the Service Application: