The black PCBs that Sapphire used for some of their cheaper 9800Pros are actually leftover 9700Pro circuit boards. This apparently limits the overclockability of those cards, but they still run at stock 9800Pro speeds just fine.
Generally speaking, differing PCB colors mean very little, if anything. Those particular Sapphire cards were a special case, since they used a nonstandard design AND a different color PCB.