I like the idea of random rain effects and thunder sounds. (we could get away with just having rain effects, and no changes on the maps)
The effect of snow would be easy, but actually making snow-covered maps would be extremely time consuming from what I can imagine.
Fog could be pretty interesting, limiting your FoV. (same effect as it being dark if that ever comes into play)
Hail wouldn't need any map changes, and could do random damage, but damn that would just be annoying.
A tornado would require some crazy animation which I guess could be possible with some 3D model, but that might be going too far.
And I'm not sure what nuclear fallout actually looks like, but if it was glowing green rain that slowly irradiated you, I wouldn't have too many objections.(although there's no reason for there to still be fallout almost 200 years after the bombs fell)
Not all of these need to be included, but a few of them would be a nice change.