I need to write a new article called "Don't fear ONET.XML" since that's what I'm discovering right now.

But just a quick snippet (thanks Frode !) which is worth remembering:

To change a site definition to hide the display of pages in the Navigation menu bars by default (ie. unticking [ ] Show pages in Site Settings -> Look and Feel -> Navigation)), just find this:

<Feature ID="541F5F57-C847-4e16-B59A-B31E90E6F9EA">
  <Properties xmlns="http://schemas.microsoft.com/sharepoint/">
    <Property Key="InheritGlobalNavigation" Value="true"/>
    <Property Key="ShowSiblings" Value="true"/>
    <Property Key="IncludeSubSites" Value="true"/>
  </Properties>
</Feature>

and change it to this:

<Feature ID="541F5F57-C847-4e16-B59A-B31E90E6F9EA">
  <Properties xmlns="http://schemas.microsoft.com/sharepoint/">
    <Property Key="InheritGlobalNavigation" Value="true"/>
    <Property Key="ShowSiblings" Value="true"/>
    <Property Key="IncludeSubSites" Value="true"/>
    <Property Key="IncludePages" Value="false"/>
  </Properties>
</Feature>

Easy, yet tasty.