There are two ways either by reading the registry or by browsing the file system. Both approaches have their benefits.
Reading the registry:
C++ example:
http://astebner.sts.winisp.net/Tools/detectFX.cpp.txt
C# example:
http://www.codeproject.com/KB/dotnet/frameworkversiondetection.aspx
Browsing the file system folder %systemroot%\Microsoft.NET\Framework:
http://msdn.microsoft.com/en-us/kb/kb00318785.aspx
