First off, I start preparing for my nuclear holocaust quite early in the game.
The first part of my strategy is making good use of cities that have at least some hills and coastline, so when the world goes down the pisser I will still be able to have food producing terrain. The nuclear aftermath turns everything to desert and tundra, except for hills and water.
Secondly, once I start getting units like musketeers, cavalry, and cannons, I only garrison one unit in a city. (unless that city is off by itself in injun country) I take groups of cavalry (normally 4 at a time), that I have built as my standing army, and put them in fortresses that are in mountains (or hills, if you have no mountains) and not adjacent to city squares. I spread them all over. I also stack any naval units I have in task groups, normally at least one per coast, also outside a city radius; something like a galleon or two and 3 or 4 frigates in a group. This is important, and we will come back to it later.
Now, as I move into more modern times, I have my thriving metropolises and nice shiny cities. Yay. But so do the other Civs, and that just isn't going to do it for us. So, on with our preparations for doomsday.
Our order of battle:
For air forces, each city exposed to the coast or border gets an F-15 or Jet Fighter on Combat Air Patrol (CAP). Minor interior cities, the ones that are not inviting targets (lower the population, the better) get stacks of bombers on them (at least a dozen), in reserve for homeland defense. A half dozen or so Jet Fighters or F-15's and Stealth Fighters parked as well for replacements. Older Bombers are good for homeland duty, plus some Stealth Bombers to replace losses in the Carrier groups. I get full of myself and rename these cities as airforce bases. (i.e., Chartres AFB)
The Naval forces have been evolved into Carrier task forces; 4 Battleships for escort and shore bombardment, 2 Carriers, 1 Transport, and an AEGIS. AEGIS is on anti-sub duty. On each carrier is 1 Jet Fighter or F-15 on CAP at all times, 1 Stealth Fighter for recon, and 2 Stealth Bombers for deep penetration raids on the enemy. The transport has 4 marines for opportunistic assaults and special operations, 2 artillery to support said marines, and 2 Mech Infantry should I decide to hold some ground. This all is a lot of firepower either on land or in open ocean if you use it right, and keep reconning during times of war with those Stealth Fighters. Groups of a few transports are posted in my waters guarded by a ship or two, one group for each side of my coast. These are for use to transport my tank divisions, and are, again, not adjacent to a city.
Off the coast is a screen of subs, it wont take much, nukes or oldies, to watch for approaching enemy battle groups. These subs spot enemy ships, the homeland defense bombers redline them, and the subs finish them off. This leaves the Carrier groups free to go pummel someone (I make at least two, more if production permits)
Land forces; one Mech Infantry per city. Yes, I hear you out there saying you want more smiley faces or more protection, but theres a reason for it. I might put 2 in a city thats off on its own as an outpost.
Outside the cities are my main forces. Fortified in the hills and mountains, I have a group of 2 Mech Infantry and one Artillery scattered about for every 8 cities or so. These are my National Guard, and are mobilized via rail to contain invasions. Along with airpower, they will stop anyting on the beach or in the mountains smaller than a bunch of armor, and we have subs to spot and sink those kinds of things before they hit us, right? If you share a border, do regular recon overflights to also spot incoming forces (one major nuke target are the enemy railways on their side of the border, so you can bomb the crap out of their units as they come to attack you). I space my cities so enough rail remains to mobilize these troops even if I get carpet-nuked.
Offensive forces are my Modern Armor divisions, in groups of six and fortified in the mountains all about. You don't need many, really, I find that 2 groups is a good starting point. I keep 1 on reserve for homeland operations and all the others are ready to ship out, either with the waiting transports or by mass airlift over to an outpost city on another continent. Any elites are culled from the divisions, replaced with vets, and stuck into my Armies and held in reserve for use in the really arse-kicking offensives. And, you guessed it, they're dug into mountain fortresses in the boonies. Also dug in somewhere are a dozen Paras and a dozen Marines, for extra cannon fodder.
Lastly, I have fortresses guarded by Mech Infantry and containing a mind boggling assortment of Artillery, Cruise Missiles, Tactical Nukes, and a few Settlers and some workers. One of these arsenals per continent or contiguous area of my empire. The Ordnance is for blowing up invaders, and the civvies are for rebuilding my nuke-shattered empire.
And lets not forget our good friend the SDI. 'Nuff said.
Now, how does all this work, defensively? Well, when the time is right to "push the button," preferably any time you have enough nukes and they don't have the SDI, I let it rip. Target Everyone, I'll explain why later. Even if I get nuked back I still have my fully capable military, the ability to project its awesome force across the globe, and a capacity to recover my cities. My back up workers are clearing fallout, the settlers can add to cities, and even if my air bases got nuked, I should still have carrier groups to cover my arse till I rebuild some planes. Since no units are stored anywhere near where the incoming nukes will hit, I hardly lose any units, and those I do are replaced with units that were in "storage" If you're really desperate to save population in the aftermath, use workers to plant trees sacrificing production in order to ward off desertification.
In targeting nukes, hit any Civ that you couldn't crush outright with conventional weapons, and especially Civs that might be able to mount a good attack on you. Screw your allies, you're about to lose them all anyways, if you are using the right amount of nukes. Take the number of enemy Civs to be nuked, divy up your Intercontinental Missiles of Love evenly, and plaster them. Start with the capital and then work from the largest cities down to the smallest till you run out of the nukes alloted for that Civ. Special considerations are links to resources, cities with high production (large pops with mountains), and the fact that a nuke blast will alter grassland to plains, etc., not to mention hitting the other side of any borders you might have. Don't hold any back, at this point its you against everyone, so you better create a mass extinction event. If you have enough nukes, hit all the cities and then whack all the outlying terrain in a grid pattern. If you do it enough you can turn their whole Civ to desert in one turn. Make the rubble bounce.
Then what? Beats me, you can either follow up with massive invasions, or tool around in your post-apocalyptic imperial dune buggy. Enjoy.