Hi Neal
I've bounced around a few options and ended up using Ethernet for my pit. Whilst it means you have to understand a little about IP addressing it means the all of the output is completely isolated from the PC. It costs a little bit more with having an Ethernet shield for each Arduino, but you don't need that many in the bit. Another benefit is the output electronics is completely independent of any updates to the PC.
On powering the Arduinos, I still power them off USB hubs, I've found some shields haven't behaved as well as they could have using external power supplies. I don't connect the USB hubs to the PC, primarily so the sketches don't get unexpected resets doing a restart of the PC.
Cheers
Peter