Most PC games on 3.5" floppy employed some form of password protection either manual, code sheet, code wheel. Where you would find a password or codes to enter in. most of these types of protection could be cracked relatively easy and clean without affecting game play. Cracked versions were more convenient even if you have original copies of games.
If some form of preservation project gets under way i've got a decent collection of PC originals.
As I've said before, both are interesting to preserve, I imagine we could employ some scripting (lua?) with hooks into the debugger, driven by something similar to the cheat system to bypass a lot of the codewheel type protections without modifying the code.
(along with install scripts to automate that etc.)