I've examined all my cards (a variety of 7950s and 280x) and the auxillary power is not connected to the PCI-slot power. If you connect a second PSU to the aux inputs, then there is no risk of backfeed.

Obviously, i can't vouch for all cards and all VRM designs. However, I would expect that most VRM designs in use today could
be buillt so that backfeed cannot occur.

The most important thing to make sure if you are using multi-PSUs is that the ground connections are very securely connected together. In general, cards do directy connect the ground pins on the aux connectors to the ground pins on the PCI-e slot. This way, if you are not using risers, just connecting the 2ndry PSU to the aux connectors will result in a secure ground link.

The problem comes with powered risers. Theres a big danger with these, because they may separate the ground and power connections. If you connect the riser to 2ndry PSU, then the signal voltages will all be set with reference to the 2nd PSU, and if the ground voltage separate (e.g. when one PSU switches on) then this power can be conducted into the signal connectors and fry the motherboard. I killed several motherboards this way before I worked out what the problem was.

This problem is even bigger with the USB style powered risers, because they completely separate all the power, and only have a thin shield connecting the grounds - not like a ribbon cable which has about 10 ground connectors. If you are using USB style risers, you must ensure a very strong ground connection between the two PSUs. Easy way: Power all the risers directly from PSU 1 which is powering motherboard - Card aux power can come from other PSUs. Harder way: Make custom harnesses which connect the ground wires between 2 hard drive connectors. Use 2 or 3 of these to cross link the ground connections between the PSUs - don't trust a single wire linking the grounds on the big 24pin molex connectors.