The difference is that the more expensive card has a better Signal to Noise ratio.
I personally use this Newegg.com - ASUS Xonar D2 7.1 Channels 24-bit 192KHz PCI Interface Ultra Fidelity Sound Card with Complete Dolby/DTS Sound Technologies
which has better connectivity (more ports and such), and a nice shield to keep the SNR high. I can't personally vouch for low profile PCI 2.1 cards, but I can say that my Asus Xonar is absolutely brilliant. I have lost a lot of respect for Sound Blaster cards over the last few years, because I have very sensitive ears (I am a composer), and I notice a sharp contrast in audio quality between Sound Blaster X-Fi cards, and my Asus Xonar.
If you demand the absolute best audio quality, you're going to want one of the Xonar cards with an interference shield on it. However, if you can settle for slightly less, the low profile cards should serve you well.
If you decide to get one of the cheaper Xonar cards, or even if you decide to go with a Sound Blaster X-Fi, it's going to be much much better than onboard. You're talking about hardware accelerated sound (on the card itself, which saves some CPU power. Although, it's not much cpu power), MUCH better Signal to Noise ratio, better driver support, and if the sound dies you have warranty options instead of having to replace the whole motherboard. Also, if the sound card dies on you, you can just use the onboard sound untill you get your replacement from Asus. Win-Win-Win IMO