Onboard sound cards are innately bad for a variety of reasons. First and foremost is the distortion and interfearance you receive with them. Even the best onboard sound will have a fair amount of interfearance just because of how a motherboard works. A discrete sound card allows for much less interfearance and will usually solve any sound releated issues someone might encounter.
I've been building systems for a long time now and every time I've run into a sound related issue, like popping, hissing, humming, a discrete card has fixed the problem every time. You don't have to spend a great deal of money on them either these days. An Asus xonar DG 5.1 card is barely 20 bucks and comes with a headphone amp built in. There are definite areas where having a sound card is a bonus.