Amiga floppies are formatted in OFS (for older stuff), and 2 other formats that I can't remember. On top of all that the Amiga's floppy controller was very good and along with the OS let you make your own file system (wich a lot of games did).
A lot of protected games used bad sectors, reversed sections (where you had to read the data backwards!) and various other crafty methods that make the likes of securerom look dated.
To make a image of a Amiga disc you have to use a program calles MakeAFS(I think) on the Amiga and then copy the resulting image to a (hi density) floppy, burn to CD or upload it somewhere.
When on your PC you can use a emulator to read the images and play all your own games.
Sorry I'm being a little vaigue here, It's been a long time since I touched my Amiga (it's currently in the loft with about 200 games!).