Can you use: CustomMasterUrl="_layouts/xxx/todd.master"

as an attribute of the site definitions ONET.XML configuration element?

Thanks for the suggestion..
But actually I would need to have multiple masterpages.
Each site may use different master  page.

I am wondering how to load different master page. Is there any way
to do this programmatically?

I heard aboue the MasterUrl with SPWeb. But I am too sure how to use
this.

Stramit wrote a Master Page switcher that should get you going in the
right direction:
www.codeplex.com/.../View.aspx

This seem to be the solution what I am looking for, but I would need
to know one thing can I use the same master  pages with ASP.NET
(aspx) pages.

Haven't tried it but I doubt it. The #1 reason that I can think of is
that the WebPartManager and the SPWebPartManager (which WSS v3 requires)
are from different assemblies.

I’m confused… are you talking about NOT using the SharePoint provided master  page? Or are you talking about creating your own? Either way, you can still add the SPWebPartManager in your own master page as long as you add the correct <%@ Register %> tag in the header of the page.

Or am I not getting it <after a long week>?

Where do you plan to put your master  page that's going to be used for
your app within the _layouts directory? Within a gallery or on the file
system?

You can still use the tokens that are listed in the WSS SDK even if it's
not a SharePoint app because it will still have access to the SharePoint
context due to being in the _layouts:

WSS v3 SDK: General Reference \ Window SharePoint Services Sites and
Pages \ Master Pages \ Customizing Master Pages in Windows SharePoint
Services.

I plan to keep the master  pages as part of the ASPX website which would be part of _Layouts.
I will be developing my own master pages. Suppose, if I develop a masterpage called mymaster.master.
I want to use this mymaster.master with the aspx as well as SharePoint sites.