It's very strange since the Nexus One/ Galaxy S/ Wave use a Wolfson WM8994 audio chip and Ipod Touch/Nano use a Cirrus one. Audio quality on both is very similar (with the Wolfson chip being slightly superior in some aspects) the only bigger difference is that Samsungs should sound a bit warmer which might give a misleading impression that it's inferior.
Now the cool part is that Samsung used to supply Apple with their audio chips so they were both on par until they (Samsung) went for superior Wolfson ones to offer better audio quality. Their previous phones had very similar audio performance to Apple mp3 players:
http://www.gsmarena.com/latest_features-review-171p2.php
"
If you pay closer attention, you might notice a suspicious resemblance between the results produced by the Samsung handsets and the iPod unit we were testing. We were caught off guard too and we even thought we had some kind of a problem with our test setup. But after we checked on the matter, it turned out that Samsung are in fact supplying Apple with audio processors."
Now Samsung mp3 players use the same chips that Samsung smartphones use and while reading reviews you will see that Samsung mp3 players offer slightly superior audio quality to Ipods.
However both companies are way inferior to companies that are pros in music players like iRiver, Cowon or even IAudio.
This review was made when Samsung used the same audio chip as Apple:
http://www.pocketables.net/2009/03/apple-ipod-touch-2g-vs-cowon-s9-vs-samsung-p3.html
and a newer 3G ipod touch vs cowon S9:
http://www.digitalversus.com/ipod-touch-vs-cowon-s9-p974_8065_93.html
As you can see the audio quality is hands down better on the Cowon player while the audio quality on Apple and Samsung players was similar.