which I'm about to start modding, on the corner of the MB there is apparently an internal Firewire port. (It's right next to the usual 2 FW ports accessed from the outside.) I'm wondering if anyone knows what it was intended for, or what advantages it might have in a mod? I've checked all of the documentation available from Apple, and there is no mention of it whatsoever. Any clues?

don't know what it was intended for. but i know what i intend to use mine for. since i've been using mine i for a music jukebox, i bought a griffin fire wave for 5.1 channel separation

Lots of options on that.....Front fw port, built in ipod dock and or portable hd, built in camera, etc. etc.

I used mine for a harddrive.

Until I put my Sawtooth back in it's case I am using mine for an external CD-RW burner and occasionally networking with the Mac beside it. It is simply more accessible than the two on the back atm.
http://img181.imageshack.us/img181/3167/10024772zo5.jpg
:\ It has been a bit of a mess lately, but I really need a whole new computer so I can't quite justify spending $200+ for a new PSU and decent GFX.
Now you may be saying, "But wait, in that picture you have _two_ PSUs! Why do you need another?"
The answer to that is, despite the primary being advertised as 470w it can barely handle just my Sawtooth lobo and boot HD. If I add so much as the two extra 50mm fans you see on the upper half of the CPU heatsink I start getting power loss during boot and power loss under heavy use after a while. So, because of this I have to use that second PSU you see as well (a 250w Comtex I pulled from an old Comtex PC).
I can't seem to get good PSUs locally.

Kinda miss the "good old days".
http://img259.imageshack.us/img259/1831/10022482md8.jpg

I remember reading somewhere it was for internal storage and presumably hard drives where going to have the interface built in but nothing ever came of it and thats why it was the first and last to ever have an internal port.