Have you tried using good, well shielded speakers? I have had noise on sub-standard or poorly sheilded speakers. Price is not always an indication of quality when it comes to speakers, since the ones from a few years ago usually sell for a song today. I have a pair of Cambridge Soundworks speakers at home, mid level, that have no noise when connected to any devices and ran in the $100-$125 range. I picked up a pair of the top end ones not too long ago that will be going onto the computer, so that the lesser ones can go onto the music works system that I picked up.
On the other end of the spectrum, I have a pair of Yamaha computer speakers that I use for my iPod at work that ran about $40 or so when I picked them up. No sub-woofer on those, which is why they are that little. Any three speaker (or more) system that runs less then $100 makes me question the shielding of the units.
There could also be some stray electricity in your area causing the noise. If possible, try putting everything onto a good UPS system. If you are in an older house/apartment building, it could be the wiring there. New construction (in the past 10 years or so) should be fine. In my old place, I had horrible sounds, whenever someone turned a light on or off, come through the speakers. In the new place, I had a new line run for the computer system as well as the AC (when I need it in the summer) put onto a new breaker. I still get an occasional pop when something cycles, but not nearly as bad as the old place.
You also might want to check and see what else is on the same breaker as your computer system. If you can, put it onto a less used one (might mean relocating to a new room). Since you say it happened before, that could be the issue, unless it also happened in another residence. It also could be that the shielding on the secondary audio card is better then what Apple uses for it's internal. Is there a reason why you don't use the audio card for all your sound needs?? I have only used the stock Apple audio in my Mac's since I was waiting for the soundblaster card, and then I sold my tower. I might get something when I get the new tower (hopefully soon after MWSF next year) but haven't decided just yet.
