Copy Protection Used on Atari 8-Bit Computers
Background
The Atari 8-bit computer systems communicate with the disk drive over a high-speed serial port, making high-level requests for sector data only. For this reason, the disk drives are essentially a complete stand-alone computer. Early drives were single or double-density 5.25" using FM encoding, all the way up to 3.5" DD or HD drives using MFM. Most original software for the system using copy protection was released on single-density 5.25" disks.
A common add-on to the Atari disk drives was the "Happy" modification (and clones). This replacement firmware and RAM expansion allowed much more control over the writing process of the drive, so it foiled most copy protections of the time.
Bad or missing sectors
Since the Atari only requests sectors from the drive, and the disk drive firmware will not allow writing "bad" sectors, original software contained (or were missing) sectors with errors. This could not be copied with standard firmware without physical tricks (such as writing the sector over and over while the disk drive door was opened or pressing your finger on the disk to stop/slow it.
Sector Timing
When writing to the disk drive, the user also has no control over how the sectors are written to the drive. The copy protection could measure how long it took to load one sector and then another and measure the time difference, which would be different on a copy vs. the original.
Duplicate Sector Numbers
During mastering, a disk could have two copies of the same sector on a track with different data. The protection requests this sector from the drive and if it is the same every time, it knows it is from a copy.
C64 Serial Registry