I am working on updating the list to match the changes done in version 188.8.131.52. When I am done I will contact Raze and he will update the three first posts of this thread (+ the title). You can expect to see the changes sometimes tomorrow. I think.
Note: You are still welcome to post changes you encounter. I am aware of the following:
Skulls can be crushed again with a Mortar and Pestle to create Bonedust.
Ancient Human Skull can be combined with Pixie Dust to create a magical variant, which in turn can be used to create amulets, belts and rings.