Actually, yes; off the top of my head:
DS9: 'The die is cast' - A romulan/cardassian fleet is in the process of turning the founders' home world into rubble by using photon torpedos and disruptors.
Voy: 'The omega directive' - Kim puts enough antimatter into a photon torpedo warhead to, in his own words "blow up a small planet".
Hm, so it seems to me that the usual photon torpedo is
not a WMD. It's like a missile. It's only a WMD if you put a nuclear warhead on top of it, but in general, it's just a conventional missile.
Is a conventional bomb a WMD just because you can drop a hundred thousand of it on a city? Or is dynamite a WMD because a large enough pile may be able to destroy an entire city?
The usual photon torpedo is only able to blow a small hole into the ships hull, even if it explodes inside (as seen in TUC). You
can modify the warhead, but that's seems to be the exception.