overall n900 is the best best in comparision in performance vise! but availability of the applications is low at this point.
But S60 v5 software of N97 is being elder by an year it has some advantages in applications sector
the camera quality is same for the both devices and in music N97 is the best as there is no equalizer setting int the N900. and the there is no portrait mode in all screens of N900. but these problem can be changed by an software updates but nokia is updating the phone software fast. As in the last week only Nokia given two software updates over the air for N900.
But it always the user preferences and choices that matters. For greater multimedia function go for N97 and for greater connectivity options and great web surfing go for N900