These are what i experienced on some of the projects i have worked on:
1) Scripts,Styles,Fonts,Layouts needs to be published.Because they stay as draft items in your “_catalogs/masterpage”
2) The lists that use filtering needs to be updated.Sometimes it bugs out.
3) If you have used NewsFeed in your portal,its contents need to be deleted from MicroFeed special list.Just click on the guid item and it will show the users posts.This is important because people will see users’ posts from the test environment
4) Never ever use SPContext.Current.Web.List(“blabla”) to access lists.Its one of the evil reasons your users getting permission problems.
5) If you have used database connections in your code,update your web.config.Backup&Restore doesnt backup your web.config
6) Always backup the live server through powershell script in case something goes wrong and you may need to restore later.
Will update this post as i see fit in the future.