That is essentially what I did; however, there are a couple small potential problems I discovered with your kind of setup...
USB ports provide a current limiter on the 5V line that has a maximum output of 500mA. They also provide a capacitor to prevent spikes on the 5V rail as a device powers up. If you connect your usb ports directly to the 5V switched power rail (as from a moles drive power cable) you could potentially have an unregulated device (such as one of those USB "cell phone chargers" or the like) damage your system if you use such a thing. You can also have the problem of a USB device causing your computer to reboot as it powers itself off and on and that power cycling causes a large enough voltage dropout on the 5V rail.
I experienced this second problem quite often and at unexpeted times. The final problem is that the USB controller is allowed to dynamically manage current to the attached devices. In theory, this makes a difference to some devices that go to sleep based on the amount of supplied current. Running them off of a constant source shouldn't pose a problem, though it wouldn't be unthinkable to assume that there are problematic devices or drivers out there..
I solved the problem by switching the 5V USB lines with cheap reed relays. They are rated at 500mA (the maximum you could draw from a USB port anyway) and they only cost about a dollar. The USB ports 5v power from the motherboard is run through the relay and the relay is switched by one of the normal switched power rails. This ensures that the USB device power is always managed properly by the USB controller, but the power is always switched off with the PSU.
Also note that the power is still supplied to the Serial/Parallel ports on the EPIA no matter what, though most serial and parallel devices do not attempt to draw power over the ports...



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