This is more of a hardware suggestion, but I have found an advantage/reason to install a PCI firewire card. It allows one to turn-on and off devices selectively without worrying about the other devices in the chain.
I've got a couple of external firewire hard drives which I use occassionally, but aren't worth leaving turned on. When they were chained together off the built-in firewire port, I always had to worry about whether to power up everything in that chain.
This also means a quieter office, since there are that many less noisy cooling fans! I only use firewire hard drives, so I don't have any experience with the vagaries of firewire devices running from a PCI card vs. built-in port, but this may allow you to save those precious built-in ports for problematic firewire devices.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20030804135753984