To summarize the answers and what I’ve found so far, here are some good links to answer this question:
- Encrypting Configuration Information in ASP.NET 2.0 Applications – 4GuysFromRolla.com
- How To: Encrypt Configuration Sections in ASP.NET 2.0 Using DPAPI – MSDN
Please feel free to complement with other links, maybe some to WinForms- or WPF-applications.