Q. Can a SharePoint master page have a code behind file?
A. Yes. A SharePoint master is not different from an ASP.NET master page except that it has controls specific to the user interface of SharePoint. You can have a code behind file for a master page.
Q. Can we have nested master pages?
A. Yes. You can have nested master pages, and they provide great flexibility in defining a UI that is mostly consistent and at the same time slightly variant across modules within the application.
Q. Can we embed web parts in an application page?
A. Web parts can be embedded like any other web control within an application page. However, these will not be editable and cannot be configured through the user interface.