Well, I like putting Missiles onto subs and Missile Cruisers since they're cheap to build.
If you don't have an invasion force handy, you can use these to buy you some time. I like using subs to blockade enemy territories or watching for incoming attacks. In the meantime, I can get my fleet and invasion force into position. Of course, if you're smart, you could borrow from real-world militaries like the US military and set up something similar to what the US Navy and Marine Corps do. The Marines are using what's called a Maritime Preposition Force (MPF). Thus, I have my invasion force (say, minimum 4 Transports fully loaded with Marines, Tanks, Helicopters, Transport Helicopters, etc.) with an accompanying fleet (say, 1-2 to Carriers with 1 Battleship, 2 Destroyers, etc.). The Submarines would already be in place to watch for enemy ships that might attack my invasion force/fleet. Since they are carrying Missiles, I can launch ahead of the killing blow to weaken the enemy ship to minimize damage to my own vessels--crucial for a sustained conflict where you don't have time to lose tempo repairing a ship. Meanwhile, my MPF moves into position. The Fighter Jets scream overhead and weaken the enemy to prepare for Amphibious Assault (which, btw, seems to be better done with Tanks than Marines, which I find hilarious).
I could also use the Missiles to weaken city defenses without hurting my own units, etc.