Werebeasts are building destroyers, and will gravitate towards buildings to destroy. "Buildings" includes doors and (S)upports. Build a door or a support with a 5x5 layer of floor tiles on top, which aren't connected to anything else. The werebeast will destroy the support/door and the floor tiles will cave in on them. (NOTE: if you use a door, remember to LOCK it, so that your master weaponsmith doesn't accidentally open it.) If you have an artifact support or door, even better: the werebeast will make a beeline for the artifact, but will only be able to deconstruct it, not destroy it.
Have the most direct available path into your fort be an area with drawbridges at either end, and when the werebeast enters, close both drawbridges. Works best if you have some statues or some-such in there, to distract the werebeast to give the doors time to close. (Artifacts work particularly well as bait).
Variation of the above that I discovered by accident: When I have an area off of my entrance path that's not connected to anything else, but that has a Butchershop, a Tannery, a Fishery, a Carpentry shop, and a Boyers shop in it, the werebeast tends to wander into that area and get distracted destroying all the workshops. Often stays busy for long enough that it transforms and wanders away on it's own. Or, you can have a drawbridge at the entrance to your bait-room, and close it while the werebeast is destroying everything.
Another way to take advantage of the building-destroyer tag: Floodgates are buildings that can be destroyed. Floodgates can have magma behind them. (Just make sure it won't flow over any masterwork engravings. And use a magma-proof material for the floodgate)
Various other traps, such as pit-traps (a draw-bridge on the floor that can be manually opened while the werebeast is on it) are possible. Or, a drawbridge that when it's opened releases a flood of magma into the hall.
Or, get creative with very over-elaborate-death-traps. In dwarf fortress, the answer to any problem is always "more magma" with a side-helping of "over-elaborate death trap"