Oooooooooooh... awesome, thanks for explaining that, people. I didn't realize the special effects category was so all-encompassing. So if you shot someone in the cyberfoot as an attempt to disable the foot, would they still take damage? What kinds of modifiers would be involved in trying to hit something as small and usually mobile as a foot? What would the effects of a shutdown cyberfoot even be? You can't walk? seems unlikely, it'd just slow you down some.
1) I'd say yes, since it's part of their body that's taking damge.
2) -3 or so, I'd imagine. It's not quite as hard as shooting an eyeball, but, it's still not an easy target.
3) I'd say almost completely immobilizing, for the purposes of combat. It's really hard to walk with 15-20 pounds(that's being conservative) of dead chrome on your leg, let alone the outright pain and such of walking on an ankle. Atop all that, it doesn't just turn 'off.' A called shot to the foot would likely mangle it to Hell and back, tear it apart, and leave you dragging a whole bunch of pneumatic components and wires about. In the absolute least, I'd impose a -4 penalty on tests requiring the wounded foot or -2 and call a balance check on the player every time they did something. Getting 'shot in the foot' is still pretty damn lethal.
That said, I also run pretty lethal games.