get a SB Audigy or higher end sound card
I woiuld suggest getting a higher end sound card. One of the problems with lower end sound cards (and crappy head units/amps with low RCA voltage outs) is that they are too close to the sound floor. Their RCA voltage output is usually low like 2volt or less (many onboard motherboard sound cards have a Signal to noise ratio of something like 85 dB or 90 dB or even worse, while a SB Audigy is 109 dB and have an RCA voltage out of something like 7volts! - better than most head units!).
The further away you are from the noise floor (read higher RCA voltage) the less likely that you will have noise through your system. Higher RCA voltages and higher S/N ratios have allot less problems with noise. Your amps and/or head unit must be able to accept a high voltage as well, or else your amp will experience clipping or distortion. As always, start off with setting your amp gains LOW - higher RCA voltage will allow you to have an car audio performance without noise. On lower end head units lower RCA voltages will cause you to have to turn up the gains to get decent volume. As always - stayaway from crap and you get what you pay for. Never buy Pyle, Pyramid, Legacy or Jensen (lol, pimp my ride put CRAP jensen car stereo equipment in this girl's convertable on the last episode - but then again a great install can make even crap equipment sound decent)
Also if you don't have an amp with an RCA input, then trash your factory head unit and get a high end head unit with high RCA voltage outputs (like 5V or the newer Pioneers that are $200 or more have 6volt on most of them).
If you're broke, then just use an FM transmitter. Since FM transmittors break group loops (since radio waves can't conduct electricity), you shouldn't have a problem with noise.
1: get a high end sound card. SB Audigy 2 ZS, M Audio. If you have a low profile case like me though, you'll be limited to a SB Live 7.1 since regular PCI cards won't fit in most low profile cases.
2: Get a mid range head unit
3: Use a multimeter - check you resistance on you groups for your amps. It is best to ground all amps to the same point using the thickest wire you can afford. Lower gauge wire has lower resistance = less noise typically. If you have different grounds, then consider purchasing distribution blocks (www.knukonceptz.com had cheap blocks that are awesome quality) and grounding everything to the same point. Limit your "bumpin" with your carputer on unless ifd you have a high output alternator (no caps don't do crap - caps don't supply more power constantly - just instantly for 1/2 a second).
4: Upgrade "big 3" power wires under your hood (battery to ground, alternator to battery and battery to main car distribution block).
That's all I can think of. I bet getting a new sound card will solve it though.