- Encrypting and Decrypting Configuration Sections (ASP.NET) on MSDN
- Encrypting Web.Config Values in ASP.NET 2.0 on ScottGu’s blog
- Encrypting Custom Configuration Sections on K. Scott Allen’s blog
EDIT:
If you can’t use asp utility, you can encrypt config file using SectionInformation.ProtectSection method.
Sample on codeproject:
Encryption of Connection Strings inside the Web.config in ASP.Net 2.0