First of all...when moving a hard drive to another system (for file access), it's normal for certain files to be unavailable immediately. These are the files which appear under the C:/Documents & Settings path.
All other files should be easily accessible...and these files also are easily accessible, by employing a procedure known as "taking ownership."
How to take ownership
of a file or a folder in Windows XP - http://support.microsoft.com/kb/308421
There is no impact at all on programs...a given program can access a data file of any type at any time....unless we are talking about the small group of data files that appear as My Docs, My Music, etc.
So I have no idea what you are talking about when you say that programs will not open...no changes were made to programs or permissions re such.
If you did something other than the procedures detailed above...then you need to let us know exactly what you did.
The only thing governing the functionality of programs on a hard drive...are registry entries relative to Windows or installed programs. If neither of those have changed...a hard drive can be moved a zillion times (from system drive to secondary drive and vice versa) and as long as the registry and installed files are as they were when the drive was moved...the programs will function properly.
<<All of the data is still there, it's just that I can't get to from within the programs that use it.>>
Which installed programs...cannot access what data files, please?
What is the error message received when access is attempted?