Apple II copy protection was a really interesting thing. While floppy controllers were partly hardware/firmware devices, Apple II floppy disk controller was incredibly simple and most of the work of reading/writing was done in software. This meant that copy protection schemes for the Apple II could utilize a LOT more clever and difficult tricks such as custom data encoding, half tracks, empty tracks, bad crcs, bad addressing headers, etc.

As time has gone on, original Apple II disks are becoming more and more scarce. Even worse early cracking efforts often hacked the games in ways that got around disk protection, but also removed or broke things. Unfortunately, that meant removing opening cut scenes or other game-altering changes.

The 4am Archive on the Internet Archive is an attempt to back up those original copy protected games as they were. So far there are 1673 Apple II titles safely imaged.

4am has even been interviewed by Paeleotronic on how and why he went about this. He even provides some of his tools like Passport.

Definitely give the interview a read and also check out some of the games on the archive. Many of his images (like Maniac Mansion for Apple II) come with a text file that gives all the details about what protection was found and how he worked around it.