I was just discussing it here: http://www.head-fi.org/forum/thread/498063/do-my-motherboard-s-spdif-outputs-go-through-the-onboard-sound-card/30#post_6726008
PSU quality, galvanic isolation from the computer, they all affect the SQ.
soundcards like the stx/halo xt use a $2 IC and call it a "top range headphones amplifier"...this is a major lie.
an internal soundcard suffers from:
-EMI/RFI hostile environment
-shared ground with the other components
-high ripple from the ATX PSU
-lack or room/thickness so manufacturers are forced to use integrated components
-and more reasons I'm sure 
and if you meant onboard sound, these are ASIC's that are supposed to do everything at once...they do it all, but very poorly.
a RMAA measurement on a Realtek: http://www.mediafire.com/?tuy3myzu1my
and on a DAC running off a linear regulated PSU: http://www.firestone.idv.tw/rmaa/spitfire.htm
Edited by leeperry - 6/20/10 at 4:38am