It won't hurt anything.
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I have used many three conductor power cords on gear that has two pronged EIC with no ill effects. I have had many more problems using two conductor, ungrounded power cords (hum...).
Member Subaruguru used to sell his "ErnieM" power cord kits with a nifty external ground wire connector that could be either connected or disconnected to enable or disable the ground wire. That's a cool feature you might consider. I have not seen him post his kits in a long while, but I'm sure he'd help you out if you sent him an email through the Audiogon system.
Subaruguru isn't answering emails any longer..at least not mine.
Do a search on google for "bob crump asylum" and you'll end up at diyaudio (I think), it'll give you all you need to know about building a pretty reasonable PC. Another option is VH Audio...he has some good recipes and parts to go with them. Yet another option is Jon Risch's recipes, see AA or google him.
I'm currently assembling powercords and an outlet box with power conditioning...shoot me an email if you need suggestions on where to get what parts.
Jwpstayman - Why is it beneficial to leave the ground connector detached at both ends? I would think that if the ground is connected at one end, it just goes along for the ride, but doesn't hurt anything. Have you any experience with doing this, or know any theory behind it? I'm wondering because I have Atmasphere amps, which come with 3 conductor power cords, but the ground is not connected inside the amplifier. I haven't played with power cords yet (I dread having to audition yet another whole category of components).
The risk in doing what you suggest is that someone will think the cord is grounded when it is not, which could lead to problems (including safety) if used on a component that needs a grounded connection. For a 2 conductor cord, maybe use a 2 conductor plug, or (if highquality 2prong plugs don't exist), maybe cut the ground pin off the 3 conductor plug to avoid confusion.
I agree with Tvad, Connect the ground wire to the male plug as well the IEC female connector. In the case of the two wire cord application the ground wire may help bleed off EMI noise.
And from a safety aspect, because you are using a three wire plug and a three wire IEC connector the cord should also be a three wire.
Make sure the polarity on the IEC connector matches that of the male plug. Very important.....Check continuity of the plug and connector after building the pc.
Honest1- the reason that your amplifiers are "safe" is that the ground goes to the chassis of the amplifiers. Remember, grounds are installed for safety reasons, not for "audiophile" reasons - IF you are not going to ground the power cord at the component end - then you should not have the ground connected at the outlet end. If you are worried about future use of the power cord, snip off the ground pin at the wall plug end. Just my two centavos....
Regarding that 3rd pin.. The proper way to hook everything up is to use that 3rd pin on the preamp, and then no 3rd pins on anything else. Also - get a VTVM. With only the component being test, plug it into the wall using a "cheater" (a 3 prong to 2 prong adapter you can get from the local hardware store. If one spade is too big - file it down) (no interconnects attached)measure the leakage from the case to a ground (screw on the outlet, radiator, etc). Unplug the power cord from the socket, and reinstall it 180 degrees reversed (upside down). Measure the leakage again. Use the plug in the position that has the least leakage. Mark with red nailpolish the right side of the plug, and put a red dot on the outlet on the right side. Do this for all your components. It may be that you have to use the cheaters to keep the plug in its proper orientation, but don't. They sound terrible. Instead, saw off the ground (3rd) connection, or remove the plug and install another with the correct polarity. This will minimize gound leakage and really open up the sound of your system.