Yes, I remember using COA2 long ago. It does what you could do manually by searching the registry for (for example) 'c:\windows' and substituting 'c:\window' if that's what you want it to do. It will also search in the same way through .ini files and .cfg files and .txt files.
So far, so good, it will take you a long way very easily. however, lately, programs have tended to save their specs in all sorts of weird and wonderful ways, such as .dat files, .xml files, fully encrypted files and so forth. In other words, it may not fully solve your problem, but those programs that kick up a fuss can of course be reinstalled. Although not taking good care of CD's probably means they are lost, or plain illegal installs in the first place.