I think it depends on where it was bought too....
We never got the 3rd gen in the UK, so all of outs are Japanese Imports..
As such the colour choices and spec lists are in lime with what was popular in japan at that time..
Colour wise Black didn't seem very popular, so for us Black Is quite rare.. but there are way more in that "interesting" sky blue.. most seem to be burgundy navy blue or dark green.
They also had a different range of options, and less of a "fixed spec" than the Export 4Runner.
I think that rarest option I've seen is the interior roof mounded factory air purifier.... they also did a GPS version of the roof mounted field monitor.. along with the other JDM type stuff... auto rear mirrors, mock carbon fibre trim, electronic hard/soft damping etc. they also had an alternative instrument cluster that looked pretty cool... more like a Lexus style one with cold cathode lighting (I think.....)