Is there a purpose to putting materials into the guild treasury? I've been searching through the forums and the community wiki to see if there was a purpose to it, but so far nothing has come up. I sincerely hope that there is/will be a purpose to it, as it currently feels like a "black hole" - stuff goes in, but never comes back out.
They're used when making boss trophies:
http://wiki.spiralknights.com/Armero_Alchemy_Machine
Unfortunately you can put materials in that aren't able to be used by this.