If you're talking about a boot drive than i would say sata or scsi, maybe you can do pata but i haven't seen it. (prolly limited by cable length)
You can probabally boot of a usb hard drive but i don't know if i'd trust usb for my primary. If anyone has done a usb boot drive how is the performance?
Use SATA (get an enclosure with USB2.0 for Portability and SATA for speed); if you don't have an external SATA port then simply get a SATA PCI port extender to give you an external port using one of your internal ones:
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