I'd agree that trying to pull power from a PCI connector is a bad idea - if you want to do it properly, the best thing to do is to find a PCI extender card (Digikey/mouser carry them, most places that sell computer server parts also carry them, expect to pay US$10-40), and hack it up. Then be sure to fuse any power supply pins, and possibly put a diode to prevent backfeeding power. Note that if you accidentally short any of the power rails to another, you're likely to *TOAST* the entire computer instantly.
If you can state your objective, then there's a good chance someone can suggest a better answer - for example, if you just need a quick and dirty -12V supply voltage at few mA, a 555 oscillator, a diode, and a capacitor are all you need. A more robust switching power supply will cost you US$5-10, be smaller, and less risky than tapping the PCI connector.