SharePoint: Add custom Master Page in Site definition

1. Go To C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\GLOBAL
Copy Default.master to another one name myMaster.master.
Edit some layout if needed.

2. Create your own Site Definition. See http://itsmesunny.blogspot.com/2007/05/creating-custom-site-definition-in-mos

3. Edit ONET.xml under C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\SiteTemplates\[Your Site Template]\xml
...
<Configurations>
<Configuration ID="-1" Name="NewWeb" />
<Configuration ID="0" Name="Default" CustomMasterUrl="_catalogs/masterpage/myMaster.master">
...
<Configuration ID="1" Name="Blank">
...
</Configuration>
</Configurations>
<Modules>
<Module Name="CustomMasterPage" List="116" Url="_catalogs/masterpage" RootWebOnly="FALSE" SetupPath="global">
<File Url="myMaster.master" Type="GhostableInLibrary" IgnoreIfAlreadyExists="TRUE" />
</Module>

4.Edit Default.aspx under C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\SiteTemplates\[Your Site Template]\xml

<%@ Page language="C#" MasterPageFile="~masterurl/custom.master"
(Note: Don't change the name custom.master to your file name. It doesn't mean that)