Although I think I'm just prejudiced against guided missiles.
I'm with you on this one! It's not that I don't see the advantages of esp. sub launched missiles, but for me it's the painful logistics of re-supply. If I have a fleet half way around the globe that needs replenishment it's just more than my poor brain can cope with.
I know that the arguments about bombers vs missiles have been done to death in this forum. Enough to say that I will stick with the bombers - re-usable, better range, bigger damage. For me missiles = one use, lower damage, re-supply nightmare, lost hammers. Now, of course, bombers sometimes get shot down. But mostly they don't. Every guided missile used is 60 hammers gone. Each bomber costs 140 hammers. Will my bombers fly more than 2 1/3 missions? On average, yes. Therefore, for me, they are the better investment. And I won't need to replace them all after a couple of turns.
That's not to say that I don't see their use as a adjunct to naval warfare/landing operations. So I will usually build a few to have them up my sleeve if needed. But I would never base my air bombardment on them.
As for SAMs on the other hand, I'm with TMIT. If the enemy has planes I want SAMs.