Executing Shell command in web server

Is it possible to execute the SHELL command in a web server?
Are there particuliar securiuty issues I mustr deal with in the WWW server ( I am using IIS)

ex:

code ....

Shell "c:\inetpub\wwwroot\cgi-bin\pgpfiledecrypter.exe 0 c:\GE\rcms_25.txt c:\GE\rcms_25.pgp"`


code ...