I think you board is a little overkill.  I run Neo-Geo games with NeoRageX just fine on an older (cheaper) mini-ITX board.  I wouldn't think MAME would require much more.  You won't find a Neo-Geo game that requires anything that fast.  Also,  why would you spend all that money on that hard drive?  You're having a full size cab right?  Is there a reason why the hard drive has to be miniture also?  If so, you should consider a laptop hard drive with a 3.5" to 2.5" converter.  That's how I did my project and it works great.  I would just use a standard ATX power supply.  I have a smaller power supply that runs around 50 watts and I haven't had a problem.
Here's my question.  Are you going to run the arcade monitor or replace it with a computer monitor or TV?  You'll have to remember that Mini-ITX boards don't come with an available AGP slot.
I guess you answered my question with the "J-PAC" statement.  
Thx for the comments. I was thinking about using that HDD because I can do updates just by unplugging it from the cab, plugging it into my lappy to do updates, and plugging it back in into the cab. As for NeoRageX, if I can run all of the Neo games on that, and if there's a good frontend to use for that emu, I'll go ahead and use that. If the 1.2Ghz mobo is overkill, perhaps I should just get the fanless 600 Mhz mobo with an onboard DC-DC converter, like this one here:
http://www.logicsupply.com/product_info.php/cPath/21/products_id/175As for using a dedicated power supply for the mobo, I'll do that, as long as I can do it neatly and not drill a hole in the back to get the cord to the power strip (might as well use a Bits Ltd. Smart Strip if I'm going this route... 

 )
Mind you all, this is just a pipe dream at the moment, but once I get around to doing this, I'll keep all of this in mind as I make my choices. BYOAC'ers are truly the best.  
