Edited by Qoweg - 6/30/14 at 8:14am
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