Some interesting ideas in here. I particularly like Fenwah's method of chaining someone up and having them beaten to a pulp by a training weapon, something only the new version really allows for.
Creating training weapons in 40d is easy - make a weapon called "training sword" (or whichever), copy it from the sword entry (or whichever), drop the damage value to about 1/10 of normal, and change the damage type to impact.
I also suggest you not give that weapon to ANY civilization (especially your own), since then, you can get "artifact" training weapons (LAME), and you have to wade through a bunch of them in the trade screen, etc. Instead, make a reaction that creates it (I made mine require wood and cloth) - this gives the additional bonus of letting you choose the material it's made of (I chose wood).
There you go, a no-quality wooden weapon that does exceedingly little damage. Actually controlling when dwarves use training weapons and switching out weapons is quite a bit of a pain, though... :-(
The reason it's only really possible in this version is because of how the body system works now. Before, you could take out anything in one or two whacks with a good hammer. Nowadays you've really got to get lucky with a blunt weapon in order to do anything other than just bruising, and you no longer have the instakill strikes to primary bodyparts like you did before. The only way to kill someone with a blunt weapon now is to either cause enough internal bleeding that they bleed out, or smash a bone in just the right way so that splinters go into something important.
And with how materials and areas work for determining damage, you can also make far weaker weapons now than you could before. But it's still mostly just the physical body reworks that makes this kind of torture accessible.