To isolate where the problem is coming from:
Unplug the jack from the audio out on the mainboard and plug it into a portable audio device (with the volume turned right down of course) see if the noise is still there. Also maybe plug some headphones into the audio out of the mainboard, again making sure the volume on the PC is down. A crackly kind of noise would indicate to me a blown input stage or something, I can usually tell if I can hear it. If you could make a recording of the noise and post it that might help.
Onboard audio on modern mainboards is usually OK, many years ago some onboard audio was truely horrible, but now days there's not much difference between onboard and external sound cards as far as DAC's go.
Maybe also a more detailed description of your setup, which speakers the noise is coming out of, what you are using to control volume, etc...