How to counter Yarok?

[crimsonking]

Yarok is a 5-mana commander, so one obvious strategy would be to stax it out of the game (with cards like Winter Orb and such). In this vibe, one option would be to play a Derevi, Empyrial Tactician deck.
Darksteel Mutation and the like are only good if your friend just casts Yarok and then passes, waiting for his next turn to bring out the rest of the pack (which isn't that great of a plan, by the way).
If he holds Yarok in his hand until he has enough mana to cast it together with some value creature, instant removals are better.
You could also steal it. There are many cards that do that at instant speed (Captivating Crew comes to mind, but there are many others), and that's a good thing to do in EDH regardless.

[Edephos]

High five to Crimsonking.  The suggestion of stealing Yarok is excellent. There is nothing more disruptive to commander focused decks.  But you must be prepared for the hate that stealing Yarok will generate.  They likely can't move forward with their game plan until they have Yarok back.

Morganator's comments are all on point.  Examine how you handle the situation from all angles. Forget how it makes you feel and focus on what you can learn from the situation.  The situation you are in now won't be unique to that Yarok deck.  Think about...  How to handle that type of deck.  How to build a deck like it.  So on an so forth. 

By the time you are done learning from the experience you will have figured out how to handle it, or the deck will become old news and the player will move on from it.  Then, ideally, you will run into another situation that impacts you in the same way, but you will be better equipped for it.  Playing with people that challenge is part of the fun.  If you aren't playing with those types of people, find new/more people.

The hard part of these situations is staying emotionally positive.  The feelings that come along with this type of situation suck, but how you handle those has to be examined too.  How do you handle the frustration at the table?  How does it effect your playing, your focus?  Play analysis and deck analysis aren't the only things you can think about while you patiently wait for the perfect time to cast Chaos Warp on Yarok.