Any application program that is found in your directory under "program files" will typically not copy, because for windows to have placed it there it created a "Registry" file, without that registry file they aren't "seen" by windows.
However any programs that are found outside of "program files"
Often WILL copy and function after doing so...
Like on my systems, I use a stand-alone mail program, Eudora, and I can actually carry that around (fully functional) on a thiumb drive and literally download my mail from any computer wiht a USB port and an internet connection and when I pull the thumb drive there is no trace left behnd.
that all being said, if you are patient you can usually grab the data files related to program settings from your old drive and transfer them, but it's tedius work requiring more patience than I believe most people have, and generally your time is better spend resetting all those values using the programs.
As for the data itself those programs are there to manipulate (documents, pictures, audio & Video) that data should never be on your system drive in the first place.
Nor should you only have one copy.
"Backups" of your system save setup time
"backups"of the data itself protect the data.