Last year, Windows Kernel team released a new cryptography libraries called Next Generation Cryptography (CNG). Although it is only available on Windows Vista and Windows Server 2008 kernels so far, I think it is going to replace the CAPICOM with its powerful new implementations.
I quite liked the new CNG libraries as it gets over some limitations of the previous library.
CLR security team released a new project on codeplex called CLR Security for that new cryptography library on .NET. So it is possible to benefit from those libraries in managed worlds as well. For a detailed description be sure to check security blog.
Also, the team is very quick to respond and provide fixes if necessary.