NO idea what I'm doing. . .
 

Ok, supposed I have installed a game on my harddrive, lets say GHOST RECON, from the retail cd. Now suppose I have downloaded and installed a no-cd patch that replaced the exe file for the game.
Now, could I burn the game directory with the new no-cd exe file to a cd-r, take the disk to another computer( which I also own), copy the disk to it's harddrive and play the game?

It seems like I could, since everything needed for the game is on the harddrive, and the cd is no longer needed because of the no-cd exe file.

What would I need to copy from reg? Would there be anything hidden?

Also NO, because most apps are compressed on the cd.
Your cd may be 650Mb or less, but the installed game could be many times larger than that.

Couple that with registry entries, temp files in other locations, the simple answer is it won't work.
Your only hope is that the game will install from an imperfect copy but not run. i.e. you can install from a fecked copy, but also have your fixed game.exe file on another cd/floppy and replace the original.