Just upgrade windows 7? No need for a clean install.
I think the reason why you can't do what you ask is that the registery and all the settings of the OS on your hard drive will be different when you transfer an installed program from one OS to another,
I remember once I installed windows XP on my backup hard drive on my desktop, booting with that OS, I tried running programs that were installed on my old drive with XP too, but there were tons of errors during startup of the softwares and almost all of them will not start!
Some softwares can be installed on a USB stick, these are mainly smaller programs such as Bitcomet for example.