For anyone waiting on me to post base master page code for WSS sites, I have gone through the process of dismantling default.master from a WSS only installation and turns out it is identical to the base code for a MOSS collaboration site. So you can safely use the one for either instance.
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Are you using this master page? It is not working for mehttp://msdn.microsoft.com/en-us/library/aa830815.aspx