Most importantly, if it became apparent that any Arab or Muslim nation were about to obtain a nuclear capability, and no other nation were going to stop that from happening, I would annihilate that capability no matter the cost, because the alternative would be the annihilation of Israel.

In the case of Iran, that poses some problems: because the Iranian capability is spread among a large number of sites, and is deeply buried, so it would be difficult to destroy or hinder. The upshot of this is that I would have to use nuclear weapons for attacks on at least several, though not all, Iranian targets.

But then I have another problem: Israel would be so roundly condemned for this use of nuclear weapons (witness the condemnation of the United States over Iraq when the US was almost immaculate in warfighting), and given that this is only the normal reaction to Israel existing, it is likely that a large number of nations would move towards sanctions against Israel. In addition to the economic damage, it would be likely that supplies of fuel and weapons from outside would almost completely dry up, and that would mean that in a relatively small amount of time - 18 months at most - Israel would be a shambles. It's also likely that Egypt and Jordan would be compelled to renounce their peace treaties, and it's not inconceivable that the Arab nations would launch an all-out war. If they did this 18 months after the strike, Israel might not be strong enough to withstand the assault.

Given these considerations, I would be strongly tempted to remove my enemies once and for all, so that they couldn't strike in my moment of weakness. The way to do that, of course, is to eliminate their armies, their political structures, and critical infrastructure that they could use to rebuild. This would have to be thorough enough to keep those enemies incapacitated for at least 10 years, because it could take that long to recover Israel's reputation and (more critically) economy and supply situation. So, if I were fairly convinced that Israel was in grave danger of attack in the aftermath of taking out Iran's nuclear capability, I would most likely hit at all of the Arab/Muslim world's military facilities and large units, industrial base, critical infrastructure (including any large cities), and so forth. Some of these attacks would be conventional, but most would be nuclear. And as part of that, I would have to strike Pakistan and eliminate their military and nuclear capability as well, because they are the only Muslim state with a declared nuclear capability, and even if they didn't want to strike directly, there's no guarantee that the ISI wouldn't give weapons to terrorists for revenge attacks.