Mark Arteaga

namespace OpenNETCF
{
   public class Utility
   {
      public static bool IsDesktop
      {
         get
         {
            // Determine if this instance is running against .NET Framework by using the MSCoreLib PublicKeyToken
            System.Reflection.Assembly mscorlibAssembly = typeof(int).Assembly;
            if ((mscorlibAssembly != null))
               return mscorlibAssembly.FullName.ToUpper().EndsWith("B77A5C561934E089");
            return false;
         }
      }

      public static bool IsDevice
      {
         get
         {
            // Determine if this instance is running against .NET Compact Framework by using the MSCoreLib PublicKeyToken
            System.Reflection.Assembly mscorlibAssembly = typeof(int).Assembly;
            if ((mscorlibAssembly != null))
               return mscorlibAssembly.FullName.ToUpper().EndsWith("969DB8053D3322AC");
            return false;
         }
      }
   }
}

Basically you check the public key of the assembly.  If you get "B77A5C561934E089" then you are on the Full Fx and if you get "969DB8053D3322AC" you are running on the Compact Framework.