Have you tried running Alcohol 53 or Magic Disc in Wine and then doing
everything from in the virtual C: drive created by Wine? Or you could go the VM
route to accomplish the same thing. I only emntion this because you are used to
them and they are Windows disks. The c: drive is found at
/home/username/.wine/drive_c. You can store as many ISOs as you want in this
location provided that your HD is large enough.

There are several good ISO programmes in Linux, AcetoneISO (from getdeb.net),
FuriusISO
(www.ubuntugeek.com/furius-iso-mount-mount-and-unmount-iso-images-with-gu\
i-tool-in-ubuntu-linux.html), and ISO Master and Kiso (in repos). A number of
programmes in Linux can also extract ISOs including 7-zip and File roller. K3b
can make an ISO quite easily.

Once you open an ISO in Linux by either mounting it or by extracting the files
then you can launch the startup file which should launch Wine. However, Wine is
far from complete which is why I suggested the VM route. With a VM you can mount
the ISO in the settings for the CD drive which is very handy. The only problem
would be re-booting each time, but it is quite quick in a VM.