A common question I receive is the following:
I have tried to save my site as a template using "Site Action" – "Save site as template" but this option is not available as soon as I enable the publishing feature. After some tries I managed to save the site as a template my adding "_layouts/savetmpl.aspx" behind the site URL. But after creating a site based on this template the new site does not behave correct. How can I fix this?
Unfortunatelly the answer for this question is: saving publishing enabled sites as a template is not supported and it does not work. You cannot use this option to create new sites. Instead you should create site definitions (..\web server extensions\12\template\SiteTemplates) and provision the new site based on such a site definition.
Also be aware that deactivating the publishing feature and creating a template of the site will not lead to a supported template! The problem is that the template would still contain all the artefacts of a publishing site like Pages library and various different properties. Creating a template of a site which previously had the publishing feature activated is unsupported in the same way as creating a template from a site which has the publishing feature activated.
Update April 24th, 2008: The same statement applies if you save the template from SharePoint Designer. Also not supported.
Update June 8th, 2011: The same statements also apply to SharePoint 2010.
Update February 26th, 2014: The same statements also apply fo SharePoint 2013 and SharePoint Online
Update April 1st, 2015: See here: KB 2492356