Something everyone should know about sound cards.
I learned recently, from installing a few more computer systems into people's cars, that sound cards DO NOT truly put out the same kind of power that a normal head unit does. True, it is close, and does work, but I have found that you can reduce a lot of "electrical noise" that the computer / car generates if you follow these few guidlines.
1. Ground your soundcard to your car's ground. Also ground your cdrom casing to the car's ground.
2. Use a ground loop isolator between your sound card and your amplifiers (readily obtainable from Radio Shack). Keep it away from any power / speaker wires, because it WILL pick up noise. The isolator removes any power supply induced hiss / noise.
3. Invest in a good Pre Amp. Audio Control makes a good one called The OVERDRIVE that can match your output from your sound card.
4. In conjunction with the Pre Amp, set your amplifier gains to their minimal settings, then set your computer volume at 3/4 max. Begin turning up your amplifier gains until you hear clipping / distortion.
5. In Windows: Mute all un-needed volume controls. Usually the mic, the modem, and any others that you do not use.
That should get rid of the noise.