Originally Posted by Vigo_Carpathian
To me it just looks like the yeast is settling. In a few more days, you should see that clear portion expanding downward.
Vigo has it. While active fermentation was happening in primary, all that yeast was in suspension, and now that you are conditioning in secondary, it is starting to settle out. Let it happen...it'll help clear up the final product.
As for the dark color, it is probably just due to the sheer volume of beer in the carboy. I've made light wheat ales that look dark brown in the fermenter, just because there is 5gal all in one place. Taking a hydrometer sample will give you a better idea of the true color.