I found this very important link that you should have a look at when you want to encrypt configuration sections in your application's web.config file. It helps not only with encrypting ConnectionStrings but also gives an idea on how to encrypt other configuration sections, how to create key containers, export them, etc ...
Strongly recommended link: http://blogs.vertigosoftware.com/snyholm/archive/2005/12/16/1746.aspx
HTH,
Regards
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