Obviously Missile Turrets just aren't good enough, as they're designed to stop harass (3-4 Muta) and not larger pushes. A large number of people will tell you Thors are the answer, and with their bonus to light and aoe this seems reasonable.
Let's take a moment to consider this. Mutalisk vs Thor.
First I'm going to need to pull in some numbers from a spreadsheet. We can see that Mutalisks get 8.15 dps and Thors get 16 dps vs light air. So already Thors have an advantage. Additionally, with splash, the Thor hits more than one Muta at a time. So this reasonable assumption seems to hold up very well.
Let us pretend we are Jane Goodhall for a moment and observe this match up in the wild. I happen to have a good match: Sen vs Demuslim (you can fast forward to 10 minutes in).
Strangely the Marine/Thor combo seems to die out to a pure Muta approach. Now part of this can be attributed to Sen's excellent play, but Demuslim is a very good player so that can't be the reason (where as Sen could stomp me with any unit). So why are thors dying?
Well Sen will attack with Muta ratios of 4:1 or 5:1, well beyond the cost ratio. Demuslim never seems to be able to field enough Thors. This is largely a result of the Thor's long build time (compared to Muta coming out of Hatcheries), and slow speed. Demuslim tries to compliment this with dropships, but those are more cost with no real combat benefit. What's more Demuslim is forced into making slow pushes against a very mobile Zerg force. By comparison, its very easy for Sen to build a lot of expansions and just get gas out of them, allowing for a more gas heavy force (remember gas is our limiting fact for building).
I won't ruin the end of the match, but at the very least we can see that Thors seem to die out to Mutalisks outside of the 30 vs 90 scenario.
So what's a Terran to do?
Well you can compliment your Thors with SCVs, but what you really need is more damage. Luckily enough there is a very cheap way for Terran to get more damage. Marines! Stimmed Marines are very effective vs Mutalisks. What's more they have no additional gas cost. What's more those Medivacs that you're carrying Thors around in really boost the survivability of those Marines. The best part is, there is no Terran strategy which doesn't allow for easy production of Marines. I'd also add that building Turrets is a very cheap way to slow down a Mutalisk attack and give your Marine/Thor forces time to get into position.
Finally, its worth noting that the first 2 points of armor do double work against Mutalisks as they reduce bounce damage as well.
I wrote this answer before Idra vs Tarson in IEM when Idra debut the "Magic Box." The Magic Box is a technique that Zerg can use to keep Mutalisks spread out as the engage Thors to minimize splash.
To execute the "Magic Box" you do the following:
- Group your Muta and send them to a location
- Tell your Muta to Stop S
- Wait till your Mutalisks spread out, they'll be far enough apart as to take NO Thor splash
- Move M (do not Attack Move) to the Thor
- Tell your Muta to Stop S or Hold H above the Thor
Note: that Thors will do a lot of damage to Muta without splash, however, this should significantly increase the Muta survivability.
I originally wrote this post to debunk the idea that Thors hard counter Mutalisks. In my rush to do so I forgot to provide a very good counter: Ghosts.
Once again let me provide viewing materia: Jinro vs Blank.
Its worth noting that all Zerg units are biological and thus the Ghost ability "Snipe" is effective against all of them. However, Ghost dps is fairly low (6.67) and only really improves vs light (13.33) and are actually more cost effective vs Mutalisks than Thors (though at lower hp). However, what really makes them work is that "Snipe." Snipe is worth 45 hp (goes through armor) for 25 energy, which means a full Ghost can Snipe 3.6 Mutalisks worth of damage (at only 1.5 the cost). What's more Ghosts have a faster build time (40s vs the Thor's 60s); are built out of Baracks (so synergize nicely with MMM play); can be healed by Medivac; and even go invisible to get the jump. Finally, when compared to Marines, Ghosts are NOT light (they have no armor type) and have 100 hp (twice the hit points), so aren't as susceptible to banelings (though are very weak against Muta into Roach).