Site Master Page: The site master page will be used by all publishing pages.
System Master Page: Use the system master page for all forms and view pages in this site.
Look at the Page directive in master page, MasterPageFile setting that will usually be one of the following:
"~masterurl/default.master" means the page is using the system master page
"~masterurl/custom.master" means the page is using the site master page
Refer:http://msdn2.microsoft.com/en-us/library/ms476046.aspx
