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It should be theoretically better. If nothing else you'll get less crosstalk from all the other components that are near the onboard audio chips of a motherboard. But honestly. I'm pretty picky about my audio and for the most part onboard audio is just fine. It often helps to make sure you have unconnected line/cd/aux in ports muted in your mixer panel though as that will increase crosstalk from the mainboard. With the volume maxed and no signal input you can often hear clicks blips whirs and other assorted noises from the mainboard doing something, this happens on cards too though as it'll pick up bus noise.
If you have good headphones though you may want to consider an external amplifier, preferably one that's output is DC coupled. The amplifiers of both onboard and offboard audio cards generally put out crap for power, and they shouldn't be expected to as they're supposed to do signal processing not actually drive the audio device itself.
So basically, an amplifier not the sound card itself is going to be your biggest point of possible audio improvement.
One addition area of looking into might be USB based sound cards, which being physically separate from the PC are immune to the bulk majority of it's interference in the first place.