There was quite a discussion about this about a week ago. (The tread is probably on page 2). Some poeple turn the Manhattan Project into a commerce wonder or something so that they can play Civ sans nuclear weapons. That camp says nukes remove strategy since you can just nuke enemy cities and roll your armour right in. Some say nukes in Civ are underpowered as modern thermonukes will wipe out cites, not cut their population.
I tend to agree that SMAC style planet busters are unbalancing and could actually get quite boring. The Civ nuke is probably about right for gameplay - even if not an accurate reflection of reality.
