Hi,
If you search google for encrypt web.config section, you will find lots of information about how to do it, including this article.
I don't think you can encrypt individual settings but must encrypt an entire section. In this case you would have to encrypt the appSettings section and you would have to remove the file attribute <appSettings file="user.config"> and keep all settings in the Web.config file instead of using an external user.config file. This will make it a little more work to manage upgrades because you always want to use the new version of Web.config and will have to re-apply your custom settings to the new version and re-encrypt it.
Hope it helps,
Joe