For DOS floppies, I make a disk image and store the files to zip.
The disk image is in case I missed anything, or if the diskette
is bootable. The zip file is for normal file manipulation. With
CD-ROM space so cheap, why not do both?
The particular archiver I use is dd under linux, or fdimage, loaddskf,
or any other archiver that makes a binary image of the diskette.
No compression or meta data ... I can tell what type of disk it was
by the resulting size, and I can compress with zip or gzip.
The raw binary images are mountable under Linux.
For copyprotected diskettes I'm using Teledisk, although I don't
trust it entirely. Teledisk is also good for damaged diskettes,
which the raw binary formats can't handle. (The damage looks like
copy protection.) The downside to teledisk is the portability ...
I'll need a DOS machine forever to read the data. I don't have this
problem with the raw binary images.
Has anybody used CopyIIPC and Snatchit? That's supposed to work too.
It's an old pirating technique, but it is applicable to archiving
copyprotected disks.