DLC, Better Citieas you add after extended FCOM (FCOM+++) is installed (WarCry, Bobs Armory, etc.)
The animations I personally instal after Deadly Reflex because this way Seph's hand to hand and DMC Stylish override Skycaptain's animations
and you can enjoy the new animations with Skycaptains effects...
Same about amazing jump (I strongly suggest DMC Stylish Jump which comes with feminine and masculine versions - same author as the great GMC Stylish!)
Environment mods (weather, water, Vegetation, grass, trees, sky etc.) come after FCOM
Sound mods (Storms and sounds etc.) come after environment mods.
Then come independent quest mods.
Then come magic (LAME, SM, Midas) mods
As for DarkUI Darn or Darnified UI, they should come after you install your character development mods (KCAS and the like) so that Darn can override their menus
Physics and Force I install after body replacers (Robert, UFF, HGEC etc.) and mods adding armor/clothes for body replacers as they change the skeleton and thus override the effect of Physics and Force.