Just saw X2!
Not to spoil, but there's a great scene where Logan gets shot--classic comic book stuff!
Now, to answer the lingering what-weapon-on-Wolverine question . . .
If my encyclopedic, geekified knowledge serves me correctly, Marvel editors over the years have agreed that the one sure way to send Logan to the gods is with a missile strike, followed by swift decapitation while his overloaded healing factor shuts him down for a while. Next, removal of the head SEVERAL FEET AWAY from the body is required (I assume something funky would shoot out from the neck and retrieve the head--hey, it's comics after all).
At that point, Logan is dead.