firewire might be a good idea, but i think it's more of a marketing angle then practical- i don't know any that would jump to firewire, we're really looking at RAID and SCSI at the moment. definitely a RAID option as it's becoming much more practical.
the diagnostics LEDs in a convient place would be nice. also what i haven't seen that would be nice is an optional slot plate that you could plug in and read the diagnostics from the outside- much like an addon USB card, etc. i don't know about anyone else but i've always thought that'd be a good implementation, and since i've got so many extra PCI slots free i wouldn't mind losing one to a USB/dianostics plate. the USB plate is a must though, MORE USB =)
please try to include more fan headers- 2 near the CPU would be ideal for the aftermarket HSF we all use and the exhaust, one near the bottom for intake, etc.
most importantly i think would be organization- we need space for large heatsinks, not having to worry about capacitors or memory slots in the way. last thing i want to to worry about ripping off a capacitor while installing my alpha 🙂 also a power supply near the top and lined out of the way, horizontal install of vertical and inbetween the CPU and memory (what the hell is w/ that MSI? 😉 )
full manipulation through the bios with an accurate temp reading would be ideal. this includes voltage/multiplier/fsb, etc. a good fail-safe secondary bios would be ideal in case something happens, most notably BIOS flash failures and bad configs.
that's all i can think off of the top of my head, i think. SCSI would be great but realistically i think that would make the board more expensive then i'd care to pay for, however i would prefer that over an onboard audio/video anyday. i think any onboard a/v just causes problems that no real hardcore user would consider paying for.