As far as i remember marauders do additional damage against stalkers, so your best option would be a mix of zealots, sentries and stalkers.
Zealots will take damage away from the stalkers unless the enemy focusses his fire (which then would allow the zealots to close in on the marauders). The sentries reduce the damage from the marauders, giving you an important advantage. They can also block his retreat or cover yours and cut of parts of his force. The stalkers can either blink in (warning: dangerous) to quickly get in range as soon as the enemy starts attacking the zealots or - with a little micro - you can blink out as soon as a stalker looses his shields.
Another option, though more long term, would be to switch to air as marauders are ground-only and it might be possible that he focussed too much on marauders so he has little to no anti-air.
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.
Source Material
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).
Best Answer
HoTS introduced new units that force all races to have a higher variety of spellcasters on the field.
Versus Infestor-Viper you'll need Siege Tanks and Vikings of course, just as before. But since Fungal Growth and Blinding Cloud can be very obnoxious, Ghosts are now a must versus that composition IMHO.
Ghosts can EMP which removes 100 energy from a unit. If the Infestor wasn't at full energy, he most likely won't have enough for Fungal; if the Viper wasn't at full energy, he won't have enough for Blind Cloud. Snipe from a cloaked Ghost is also a pretty good counter to Infestors and Vipers.
Then it's all about positioning; if your army is out of position, he might be able to drop the combo. If he moves his spellcasters out of position, you will be able to incapacitate them.
PS: Fungal Growth is now a projectile. I haven't tried it, but the Raven's PDD should intercept the missile. Does PDD works versus Abduct too?
And Seeker Missile, since it's an ability, should not be affected by Blinding Cloud. Since they do 125 damage on impact, 3 or 4 of these in a clump of Infestors will kill most of them.