Creating a Site Collection with a custom Site Template

• First take site as template
• Site Action - > Site Settings -> Manage Site Features -> Save site as template 
• then I found "Save Site As Template" option is missing
• to bring back that option
• Deactivate SharePoint Publishing Feature (Manage site features under Site Actions)
• Now we will get Save site as template option otherwise we can access directly with below url
• “_layouts/savetmpl.aspx"
• Once done we will get WSP(Web Solution Package) file in Solution Gallery
• using Powershell OR STSAdm deploy in SharePoint
• Now we will get Template in Site Collection Custom Tab

http://neelb.wordpress.com/2010/10/28/save-site-as-template-in-sharepoint-2010-missing/

http://www.toddklindt.com/blog/Lists/Posts/Post.aspx?ID=218

http://blogs.msdn.com/b/richin/archive/2011/12/05/save-site-as-template-option-missing-in-sharepoint-2010.aspx