Some programs may cause a problem depending if they use a cd checker or not.
Most progs will work though. Windows will work that way.
Some programs can be tricked into thinking that you are using a cd by turning them into a ISO file.
Another prog called Daemon tools can create a virtual cd drive so your program thinks its in a cd also.
It just depends on the program that you have.
2 things I can think of quickly that wont work are Adobe products and anything with
Securerom encryption such as some of the newer games.
The best thing that you could do as it sounds like you are getting ready for a reload
would be to try and copy one over and try it.
You can cancel the setup as soon as it starts because it wont start if it isnt going to work.