Here is my take on countering Denial decks. There's a few different variants of denial decks, and I may not cover all. If you want to add your own advice on countering Denial decks, add it in the comments section below. Thanks -Disaru
There are a few types of denial decks, I will try to outline each one here to the best of my abilities.
I) Mono-Darkness Edit
Mono-Darkness relies on getting out pests/devourers fast, and matching the amount of pillars you put out as well. You usually draw 3-5 pillars (depending your deck), and mono-darkness may draw 2-3 devourers, and some steals. That means even if you draw 5 pillars (good draw) you might be producing only 2 overall. If they're smart and steal some of your pillars early on, you may be screwed and locked down for quanta.
Counter 1: Immolation
Ever wonder why Immolation gives 7 fire quanta and Rain of fire costs 7 fire quanta? With mono-darkness, they can't burrow their devourers. Even if your opponent has 4 devourers down and you're locked for quanta, put down a photon (no quanta required), use immolation, produce 7 fire quanta, use rain of fire, and destroy all devourers. Producing a lot of quanta on YOUR turn prevents them from taking them on their turn.
Counter 2: Rainbow/QP
Using a rainbow deck with quantum pillars prevents them from sucking up all your quanta. Even if they have 6 devourers out, that only denies 2 quantum pillars (improbable you draw only 2 QP). Even then, using a rainbow deck allows you to use play low-cost creatures and even use low-cost spells (lightning, chaos seed, firebolt, icebolt) on devourers.
Counter 3: Otyughs
Use Ots to eat up devourers. Strategy abolished. Enough said.
Counter 4: Nova
Producing 12 quanta first turn prevents the effectiveness of those devourers. Using multiple novas, immolation, quantum pillars gives you more than enough quanta and devourers have no chance of quanta-denying you.
II) Time/Earth Edit
This is probably the toughest denial deck, even I use it because it's so effective. It's key card: Earthquake. EQ is probably the strongest card of the game considering how it can change the outcome of the game with just one use, not to mention 2-3 EQs to seal the deal. It relies on denying you quanta, and if you have enough quanta to play a creature, they reverse time your creature (eternity or RTs) to make you waste those quanta. If they have 2 time pillars + Eternity, they can keep you in a lock where you keep playing the creature and then getting it reversed, and you keep picking up the same creature, having no progress. It has no easy way to counter. Luckily, it only has 6 offensive creatures (graboids) which you can use to your advantage.
Counter 1: Destroy the kill cards (Graboids)
Having only 6 offensive units means once those creatures are destroyed, you have no way to damage your opponent and win the game. You need an early way to damage graboids because once they're burrowed, you have no way of damaging them. You can try immolation + rain of fire/firebolts, owl eyes (time/earth decks have no permanent control) and even blessing+otyughs. (Reader comment: my graboids come into play burrowed. I assume you mean killing these on the turn after they morph into shriekers?)
Counter 2: Enchant Artifact
Having an Enchant Artifacts on your pillar stacks automatically gives you the upper hand against their deck, and makes 5-6 of their cards (earthquake) utterly useless.
Counter 3: Destroy (or Steal) Eternity
Eternity is probably one of the most important pieces of this denial strategy, because it keeps them in a lock. You can use deflag, steal, or even try to deny them of Time quanta (usually they use time mark as a source, so they'll have low time resources).
Counter 4: Immolation/Nova
Using a rainbow deck with quantum pillars or novas prevents them from destroying pillars, because you have none. This makes 5-6 (EQ) of their cards just plain useless.
Counter 5: Bypass Eternity *****'*** READ THIS *********
Probably the most important part of their strategy is the RT/Eternity lock. Making sure you have low amount of quanta, and making sure you can only play 1-2 creatures, ensures that Eternity can control that 1 creature you put out by just reversing it. If you play 1 creature each turn, Eternity can just keep reversing it. If you can play 3-4 creatures, then Eternity will be overwhelmed and will have to take 4 turns to reverse all of them.
The lock is when eternity makes you keep picking up the same card, preventing you from picking up other creatures or pillars. If you keep playing the same creature and having to pick it up, it's your own fault you get into the lock. If you can't pick up any more pillars, and you already have low pillar count, you will eventually lose. The way to bypass the lock is to SIMPLY PASS YOUR TURN. Don't play a creature just because you have enough quanta. Even if you have 8 cards in your hand, pass and discard the most useless card you can't play. This allows you to draw a new card next turn (hopefully a pillar or another creature), and lets you build up your quanta to summon 3-4 creatures. It's useless to play a creature if it'll just get reversed. There, the secret is out, JUST PASS YOUR TURN!!!! R.I.P. eternity lock.
Untargetable creatures (such as Phase Dragons) also bring death to the denial deck by avoiding Eternity.
Counter 6: Bone Wall
Again, if your opponent only has 6 offensive units, you are able to use bone wall to its maximum effectiveness. It delays their assault while you pick up more pillars. It always helps if you use Counter 1 in destroying graboids to build up your bone wall. Remember: All the annoying denial cards that are driving you insane (Earthquake, Reverse Time) are replacing creature cards in their deck -- Denial's attacking army is anemic.
Counter 7: Deck the RT/Eternity Deck
Decking is an easy option when facing an RT/Eternity denial deck. In order to keep you denied, they have to recycle your Otyugh/FireflyQueen/etc - forcing you to skip your draw phase. This means that you have a deck size advantage in a war of decking attrition. If they run out of fresh cards before they kill you, they lose the game. If you're playing a self-healing deck (Vampires, Druidic Staff, Miracles), you might well be able to outlast an onslaught that sputters out at 6 Shriekers. Be sure to count turns carefully in the endgame, because the Eternity owner will drop the lock and start recycling their OWN creatures once they've exhausted their entire deck, and you'll have to kill them the old-fashioned way.