How to backup programs?
When you install programs what's happening behind the scenes are a huge number of things, which can, and most likely include:
1. Extraction of zipped install files
2. Creation of folders (i.e. under your program files directory)
3. Configuration file creation and setup (if the installation for example, reads your graphics card setup & stores the resolution, colour depth possibilities for later use etc.)
4. Creation of registry keys to store extra details (file autosave paths, usernames, file locations, versioning numbers etc.)
5. Creation of start menu folders to point to your program
6. A backend data store such as a local database to save program state, entered information etc.
7. Creation, testing and storage of connectivity - for instance an ODBC Windows entry or XML file might be created, possibly encrypted with database location, password etc. details.
8. Licensing checks, license key lookups, registrations and storage (maybe to a different place than #3 or #4)
9. Possibly some permissions settings (firewall port openings, entering files or site locations into trusted lists, installation of signed certificates, Windows users who can run the app)
10. Registration of files (i.e. file information such as versioning, location, creator details etc. can be entered into the registry, COM+ or the .Net GAC stores which Windows has)
11. Windows services might need to be created to continually run or monitor items related to the program, in the background whenever Windows runs
There're probably 100s more things extra I haven't considered when writing this quick reply also. To put the answer bluntly, no you can't backup copy a program - the best you can do is to make a copy of the installation file for it. With everything moving to the cloud though, even this might not be a good idea as you'll then possibly later be installing an older version of the program and not the latest one available (with bugfixes, speed enhancements etc. made).
Edit: I should note my comments here relate solely to Windows environments since you've mentioned the program files folders above. For Linux environments, it's my understanding all applications are self contained - data is saved to local configuration files and database files housed in most cases in the same location as the program files you'll be running, so in the case of those OSs, it's probably likely you could copy the entire folder (though my comments about the older versioning will still be relevant & you'd probably then want to run an update application version-related command on each).

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