On my multi-GPU rigs, I use server PSUs like the Dell N750P to provide the 12V power to the PCI-E connectors. These PSUs do not have power switches, so initially I would just pull the power cord out when I wanted to power them down. After experimenting with the PSU control pins, I realized they have an active low "power on" pin. Instead of using a jumper to connect it to ground, I decided to use an electronic switch to power the server PSU when the motherboard powers up.
The switch I used is a common, cheap model 817 optocoupler (pdf datasheet). When current flows from pin 1 to 2, the optocoupler is turned on, creating a short from pin 4 to pin 3. For my small circuit shown above, pin 4 is connected to the PS_ON signal, and pin 3 is connected to ground on the server PSU. Pin 1 is connected to 12V (from the 4-pin 3.5" floppy drive power connector), and pin 2 is connected to ground. On the back of the board is a 1K current-limiting resistor in series with the red LED which is a power on indicator.
I also made an even simpler interlock using only an optocoupler with the pins straightened and 0.1" header pins:
