In Sharepoint 2003, creating custom site definitions required diving into the file system, copying obscure directories, editing XML files, etc.
Now, in MOSS 2007, you can create custom site templates from the MOSS interface. Create a site using whatever out-of-the-box starting template you want. Then configure it by adding or removing whatever Web Parts you need. Save that site as a template, and it will be available to you under the Custom tab in the Create Site template choices.