Took me a while to find out how to connect to the Site Gallery, so this might save you some time.

using (SPSite root = new SPSite([yourRootURL]))
{
    // DELETE OLD TEMPLATES
    List<string> toDelete = new List<string>();

    using (SPWeb web = root.OpenWeb())
    {
        SPFolder folder = web.Folders["_catalogs"];
        SPFolder subfolder = folder.SubFolders["wt"];

        using (SPWeb web = root.OpenWeb())
        {
            SPFolder folder = web.Folders["_catalogs"];
            SPFolder subfolder = folder.SubFolders["wt"];

             int numberOfTemplates = subfolder.Files.Count;
    
             for (int i = (numberOfTemplates - 1); i >= 0; i--)
             {
                 subfolder.Files.Delete(subfolder.Files.Url);
             }
        }
    }

    // SAVE SITE AS TEMPLATE
    using (SPWeb web = root.OpenWeb([yourSiteUrl]))
    {
        web.SaveAsTemplate("[Filename]", "[Title]", "[Description]", true/false);
    }
}

Credits to Serge for pointing me in the right direction: http://weblogs.asp.net/soever/archive/2006/06/28/NAnt-task-for-SharePoint_3A00_-Save-SPWeb-as-site-template-to-the-filesystem.aspx