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Blink stalkers do the trick quite nicely. Just have 12 or so blinkers somewhere near your base, ready to respond to any mutas. Having one or two HTs per base for storms is also useful. Cannons also become important as time goes on and the muta ball starts to get very large.
As for actual strategic responses to mutas rather than unit compositions, remember that he has to keep his mutas together or they are very weak. 10 mutas won't do anything useful in the lategame, so he'll be forced to ball together with 20+ of them. Take advantage of this by attacking or expanding in the opposite direction to the ball. Just sending 6 zealots to one of his expos in the opposite direction of the mutas can do a lot of damage with very little risk (worst case you lose 600 minerals).
That is out of date my friend, the more recent announcement is that blizzard think the phoenix range buff has done enough so the tempest is now going to be a long range siege unit that attacks the ground and or air from long range without aoe.
It's Blizzard so expect more changes to this unit in the future and they basically said so themselves that it's a work in progress. I expect it will change again because it's function now is almost exactly the same as the unit it is replacing (the carrier).
I do hate mass muta though, leave some high templar and cannon near you're mineral lines and hit them as they come, backup with blink stalkers.
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