Google Apps accounts allow you to define one ore more "domain aliases" (inside the "Domains" area of the Admin Console), to simultaneously associate additional domains, for no additional fee. See the documentation for details.
Thus, if your Google Apps account was initially set up with a single domain and one paid user named 'userA@domain1.com', you could then associate additional domain-aliases such that the very same mailbox could also be used with 'userA@domain2.com' and 'userA@domain3.com'.
Incidentally, Google Apps accounts similarly allow you to define one ore more "user aliases", to simultaneously associate additional email addresses for a given mailbox, for no additional fee.
Thus, continuing the previous example, you could create user-aliases 'userB' and 'userC' for 'userA', such that the very same mailbox could also be used with 'userB@domain1.com' and 'userC@domain1.com' (as well as 'userB@domain2.com' and 'userC@domain2.com', and 'userB@domain3.com' and 'userC@domain3.com').