The 80-wire cables are cable-select. Which means all the drives can be jumpered as single drives. I found out the hard way if you have only one drive on a cable it *must* be in the end connector. (cd's and dvd's don't count and will work in either connector).
This is really a per drive/ per setup thing. I've used 80-pin cables with HD's in both connectors when I set the drive up as signle or master.
IIRC on an 80p cable the PDIAG signal is still connected between the drives just like a 40pin but its broken between the drives at the host at the connector where it becomes 40/80 select.
The spec recommends that for an 80pin setup you allways attach the drive at the outmost connector. This keeps the extra connector from acting as an unterminated stub. So depending on your cable and setup you could get a case where and 80pin driver in >= ATA100 mode would not work on an inside connector.
CDROM's never really push the speed limit on the IDE bus so thats why they would work well on either connctor.