To physically transport Protoss you need the Warp Prism built in a Robotics facility. The Robotics facility require a Cybernetics core to be built, which require a Gateway (which require a Nexus) to be built.
However Protoss have a better way to "transport" new unit to the battle field :
A Gateway can be transformed into a Warp Gate (The research to be able to do that is in the Cybernetics core). A Warp Gate is able to create a new unit anywhere in the psionic matrix.
Psionic matrix is the blue area around pylons. A common tactic is to create a "proxy" pylon near the front line of the battlefield, in such a way that the pylon is near enought to be able to transport unit quickly near the enemy but far enough to not be spotted by enemy forces.
Moreover the Warp Prism (mentioned earlier) is able to go into phase mode so he can act as a pylon (and have is own pysionic matrix) but is unable to move while he is in this mode.
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
Since the last question was more about Void Rays I concentrated on more diverse Protoss Anti-Air
Gateway
Since Protoss strategies usually revolve around heavy gateway units, Stalkers are more or less a must in anti air confrontations. The most important rule of Stalkers is: unless you are chasing, never blink into battle. This is key, because as a tool, blink is far more effective as running away or chasing than it is as an opener. Stalkers are a very fast unit, so the only time you should ever feel the need to blink into an enemy is when they're running away.
Blinking away has two important aspects to it:
While retreating is often times a necessary thing, it's the latter, that makes blink such an effective tool. When you find yourself against engaged in a battle, you'll usually notice that your vanguard (front units) take the brunt of the damage. If you blink them away as they take damage, the damage will spread more evenly over your whole force and your Stalkers will continue to do damage from longer periods of time.
Protoss Air
If your build is designed around Air units there are two important things to remember:
Most people don't know the second one. The key to any Protoss air confrontation is to make it a mobile one. This is why the speed upgrade for Void Rays is so crucial. Now Phoenix and Void Ray have different use cases, Phoenix are effective against light, and Void Rays against armored. Based on what your opponent is going you have to adapt. If you're seeing Muta heavy, go Phoenix. If you're seeing Viking/Corruptor go VR. In a PvP its usually whoever has better macro or more upgrades who triumph... you know, unless you get High Templar
High Templar
Usually built out of an early 4 gate strategy, HT are one of the most powerful units in the game. Psionic Storm needs no introduction, but don't forget about Feedback. Feedback has the unit property of being amazing against unexpected units. Allow me to list a few:
I have definitely had games where I won with just HT/Zealot just because of how versatile this unit it. What's more they can easily be transformed into damage soaks (Archons) to break Siege Tank of Void Ray lines.
Having trouble against Mass Void Ray? Strangely enough Psionic Storm is surprisingly effective against Void Rays. Because of the charging nature of their attack, many players won't immediately move their Void Ray out of danger.
Conclusion
As always, the key to beating a PvP army often lies in doing something unexpected while your opponent is doing the expected. Use Observers to try and retain the advantage in the game of information warfare.