Why not attack the problem from the other direction?
Instead of trying to get mame to work across multiple hard drives,
you could make your system see multiple drives as one big drive.
Promise Technology makes PCI RAID cards that have a special mode called "JBOD".
This stands for "Just a Bunch Of Drives".
Essentially, you can connect up to 4 drives (of any size) and it will make them appear to be one giant drive to the operating system. None of your software will know the difference because it's all handled at the hardware level.
Of course, you are still ultimately constrained by the limitations of the operating system that you are using. For example, you cannot create a drive larger than 120GB (roughly).
I know the JBOD feature existed in their cards at least as far back as the FastTrack 66 card that I have.
Search eBay for "promise fasttrak".
You should be able to pick up a used JBOD capable card for under $20.
Here's one currently at $8:
http://cgi.ebay.com/ws/eBayISAPI.dll?ViewItem&item=5104269328I'd connect one drive as normal to your primary IDE port and use this as your "boot" drive. It doesn't have to be a really large drive. Just large enough to hold your operating system, swap file, and some basic applications.
Then connect the rest to the FastTrak card and set them up as a JBOD drive for all your data (emulators and roms).