Best way to archive a floppy disk?

If anything ever achieved the status with respect to floppy images that ISO has with respect to CDs, I never heard of it. It's pretty much down to however particular imaging software works, though naturally a straight dd-style image is popular. I'd recommend using the fdimage utility that FreeBSD uses for its install .flp files; at minimum you can be pretty confident you'll always be able to locate it easily for download.

(Edit: I know you're under Windows, but I wrote this for completeness)

Real men use cat(1) instead of dd(1) ;-)

cat /dev/fd0 > floppy.img

Remember that under Linux you can always use your floppy image without resorting to fossil media

mkdir /mnt/floppy; mount -oloop floppy.img /mnt/floppy