When turkey gravy sits undisturbed for hours in a clear jar, a dark layer develops at the top. This layer contains a lot of flavour but it is not fat because the gravy had been skimmed of all fat. I used the gravy for dinner, poured the remaining gravy into a mason jar and left it sitting for about 3 hours. When I went back to the kitchen I noticed this dark layer about 2 inches thick on top of gravy. I think the collagen had risen to the top.  I know gelatin comes from the turkey bones, but what is the proper name for this dark layer? 
It may not have a formal name.  If this were water treatment, we'd likely call it 'sludge'.  Although it's possible that you missed some of the fat, it's very unlikely that it would be 2 inches thick.  What's more likely is that the gravy is still undergoing some sort of settling, and that's what you're seeing:   Type 1 settling : Free-settling : iImpurities accelerate with gravity.  The oil goes up while the solids precipitate out.   Type 2 settling : Flocculation : Impurities collect together until they become large enough that gravity will overcome other forces Type 3 & 4 settling : Sludge thickening : Bands slowly form and become more distinct with time.  May require hours or days.   The exact rate of settling depends on a lot of factors.  One of the largest ones in water treatment is ionization.  (you have to neutralize any charge so that the particles won't repel each other).  Some systems use microbes to speed up the process after type 1 settling.  You have to leave it in still water for the whole time; disturbing the vessel can cause the layers to mix, undoing the type 3 & 4 settling.  (note: it's been almost 20 years since I took a water treatment class, and I never went into the field.  It's possible that terminology has changed in that time.  And when I say 'water treatment', I really mean 'sewage treatment') 