I see refuse through these goggles...
- there is refuse you should get rid of (sentient corpses that make nervous dwarfs lose hope)
- there is refuse that you can use (Bones/Skulls/hides)
- there is refuse that will rot into nothing without a hauler ever needing to touch it (cartilage/nervous tissue)
- there is refuse that will not rot but is "harmless clutter" (feathers, nails, scales, etc)
Everything I do with Refuse is done in Above/Light tiles to avoid miasma (but it is possible to create miasma-reducing systems in Below/Dark tiles).
Every system I create for Refuse stockpiles is designed with the memories of those times when stockpile systems have been jammed up with stuff like crundle scales, hair, nails, feathers, small teeth, insect exo-shells (and with reference to what PatrikLundell posted about raw-defined verse procedurally-generated creatures, memories of times that FB nails, scales, feathers, etc, jammed up stockpile systems).
Bones and skulls tend to take up too much stockpile floor space, but they are light so it doesn't matter if bone-crafters need to walk 30 tiles, so I either leave Refuse(Bones/Skulls) in the butcher's workshop or create a quantum stockpile for Refuse(Bones,Skulls) near the craft shop.
Cartilage will rot in Above/Light tiles, so it can be left in the Butcher's shop, but eventually there will be hundreds of non-rotting scales, nails, shells, teeth, and hair in the workshop and there is also the corpses of sentient creatures to be disposed of, so I create a minecart route to take sentient corpses (one stockpile), useless clutter (another stockpile), and dead tame animals (another stockpile), and dump all that junk into magma (either a long drop into the magma sea or a short drop into magma that was hauled to the surface).