IMHO the most sought after would be the LTD 175 editions that were only sold in Japan. They were produced in a number of awesome colors, many of which were produced in the single digits. Check out this link for production details: Vehicross Wikipedia Article
For the US market the Foxfire Red Mica and Dragon Green Mica were the rarest colors, with 210 and 230 produced respectively. (Except the Pearl White VX circmand mentions above, but that was a special order not a production color.) And then there are the 5-speed variants, of which only 7 are known to have existed. Two are owned by members here (etfren and myself) and five were built as race trucks. To my knowledge no one knows what happened to those five.
Here is a sampling of the JDM specialty colors:
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