Many thanks to Michael Kynoch who posted this information on the R33 GT-R Facebook page, and graciously allowed me to repost here. He explains he got the data from his Nissan FAST and vin data files. Interestingly, he came up 5 cars short; he believes they may have been painted 5 non-standard colors.
I've gone ahead and listed in order of popularity (most to least), and which Series cars they were available on.
QM1 White - 6048 [S1, S2, S3]
KL0 Spark Silver - 2256 [S1]
LP2 Midnight Purple - 2222 [S1, S2, S3]
KR4 Sonic Silver - 1860 [S2, S3]
KH3 Black 1052 [S1, S2, S3]
KN6 Dark Grey Pearl - 592 [S1, S2, S3]
BN6 Deep Marine Blue - 407 [S1, S2, S3]
AN0 Super Clear Red - 259 (special order color) [S1]
BT2 Champion Blue - 177 [S2]
AR1 Super Clear Red II/Nismo Red - 139 (special order color) [S2, S3]
GV1 Black Pearl - 19 (the very last V-spec built was this color) [BNR34 color]
AR2 Active Red/Carmine Red - 12 [BNR34 color]
Note that I take no responsibility for the accuracy of the numbers; nevertheless it gives you a good idea in general. I could not find AR2 in any of my sources, but it's likely the very last cars were available in this color, like GV1, as these colors were used on the BNR34