Just remembered this link for an FAQ on IDE:
I quote the relevant passage:
[I]5.2. Does it matter how I connect the devices to the cable?
Not much. If you have only one drive on the cable, it is best to put
it at the very end, especially when you're using any of the faster
modes. For two devices, it doesn't matter where you put the master and
the slave, or which end of the cable you plug into the controller.
Just take care that you plug them in the right way: the red wire is
supposed to correspond to pin 1.
When Plug'n'Play ATA arrives the Cable Select (CS) setting will be
used, and all of this will change. Some name brand machines may
already employ a similar setup.