To clarify:
The MDD has:
3 ATA channels (ATA 33, 66, 100)
Support for six drives (2 per ATA channel)
Slots for six drives (2 5.25", 4 3.5")
Additionally, as I read it in my documentation with my MDD, the limitation on drive size (aka the 137GB barrier) is dependent on IDE addressing, not the ATA bus. Therefore, the firmware (or OS) in (at least these machines) has been patched to resolve the addressing issue with big drives, and this patch is not channel dependent. Based on the documentation, the MDD should access fat ass drives on ANY channel. If you have a MDD, rtfm, visit the Apple support forums, and read your technotes.
With 250GB drives, and no optical drives, this means that 1.5TB is now possible in the MDD.
I am unsure, and can't be bothered to research, whether the addressing patch is in firmware, or in the OS, and whether any of this affects machines other than the MDD Pmacs.
As a side note, I see $120GB 7200RPM drives for about $120 all the time, why not buy 4 of these now, for $480, instead of paying a premium for the biggest newest drive? I did, and its lovely...