MOMCertImport.exe error: ‘The application failed to initialize properly (0xc0150002). Click OK to terminate the application.

Problem is some .NET components is required.
Open momcertimport.exe with notepad and go to the end of the file you will see this..
assemblyIdentify ........ "Microsoft.VC90.CRT" version="9.0.30729.1"

so you need to get this library install on the server (Microsoft Virtual C++ 2008 SP1)

Microsoft Virtual C++ 2008 SP1 -> 9.0.30729.1
Microsoft Virtual C++ 2008 -> 9.0.21022.8

http://www.microsoft.com/DOWNLOADS/details.aspx?familyid=A5C84275-3B97-4AB7-A40D-3802B2AF5FC2&displaylang=en

Or...
Actually MOMCertImport.exe is just add an entry of certificate to the registry so it can be done manually..
1. Check the serial number of the certificates from Details tab (mmc -> certificates -> computer account)
2. Create new Binary Value "ChannelCertificateSerialNumber" -> HKLM\Software\Microsoft Operations Manager\3.0\Machine Settings but in the "REVERSE" order
Example : serial number is ab 12 cd 34 ef 56 -> enter it as 56 ef 34 cd 12 ab
Then restart health service
R1 -> "OpsMgr Health Service"
R2 -> "System Center Management"