My '94 T-Bird had green brake fluid prior to its first flush, as did my '97 Mark VIII. Braking performance improved dramatically when they were changed over to fresh fluid.
My fiancee's '06 Liberty had brown/black fluid prior to its first flush. Braking performance improved after the flush, but not as dramatically as the above Fords with green fluid.
I just flushed the brake/clutch reservoir on my '03 SVT Focus today, and that fluid was also brown/black. This wasn't a total system bleed so I didn't expect, or experience, any change in peformance of the clutch or brakes.