I don't know if this has been done before, and when that is said it usually was, but I am pretty confident in saying that a tactical nuclear missile, which as stated earlier in the thread by a group of individuals as being cheaper to produce and less effective, could be made.
My idea, if not taken already, is that a small precision nuclear device can be fired from a naval unit with the sole purpose of launching these missiles at one particular plot. The bomb is small and drastically weaker than the ICBM, and while it does not have the capacity to kill any units in the target tile, it will destroy any improvement inside, roads and rails, and instantly and assuredly leave fallout with a 100% success rate. To make things more efficient, this precision fallout should take twice as long to sweep by workers, effectively making the tile useless for a long period and robbing the target civ of its benefits and resources.
This smart bomb should be limited though, as to not make it too easy for the better players...theres gotta be some challenge. By this I mean that the missiles can ONLY be fired from a missile-only naval unit with a limited range, say 2-4 or five tiles away from the ship. This way, strikes are more strategic and rewarding, as well as planned better than a super ICBM death explosion that leaves everyone dead and everything radioactive. By limiting its capabilites but giving it longer effect time, I can see a strategic missile being the next "Pillage", allowing you to assault a city with your land units on one side of the continent and destroy improvements for the naval capitol on the other end, to stem the flow of soldiers from the well established capitol onto the city being seized.
These missiles could provide a delay that would definitely save a small attack force on land, so seeing as how I said they were good and all, I'm deciding whether or not they should be more production-expensive than the ICBM. Thats up to Sid tho.
-The King