From a technical point of view the Amiga sound is better, of course, but I do agree that the Atari has character (and some great video game and demo music to boot)... And there is a lot of recent development of "tricks" on the Atari. For some superb modern Atari music, have a listen to Stu:
http://www.retinascan.de/phpshop/themes/kategorie/detail.php?artikelid=649&kategorieid=84&source=1In short, it's all a matter of taste, because technically all these old machines have horrible sound features.
