Many disks on the Amiga had strange sectors/tracks, or other copy protections to them... The only real way to save these is to make a image-based copy. DMS or ADF would work for many things. Of course, then, to use them (especially games) the only way to copy them back onto a disk to boot from.
I have a lot of my software cataloged as DMS (and stuff I've downloaded from Back2Roots as ADF) images on my server. Then I just pull them down on my A4000 and make them back into disks for my girlfriend's little brother to play on the A1200, while my originals are securely stored away. Not only is it safer, it's faster for me to find a disk image on my server than it is to find the actual disk in my large crates. ;-)