if the programs are on the second drive (you hooked up as slave) - NO you cannot run the programs on it, since they need to use the registry from that disk; while you are now using another registry..
you can copy data without problems, but you need to isntall the programs again.
some software that claims to do it from 1 pc to the next :
http://www.laplink.com/pcmover/pcmover.html PC mover
http://www.stompsoft.com/easypctransfer.html?SourceID=googezpc Easy Pc transfer