Well as this meta's run as omotm comes to a close, I must say that this has been one of the most fun I've had a chance to play. And as the 4th on the ladder (as of posting), I want to share what I've noticed have been effective checks and counters to most of the controversial pokemon, along with other things that do well in the current metagame.
Entei- Probably the best protean abuser along with Deo-S, Entei's ability to use Espeed to KO Greninja (if it's taken 10-15% residual damage), burn dusclops semi reliably with sacred fire, maimTorkoal with stone edge (OHKOing the shell smash set), and just being an extremely powerful physical wall breaker make him a great revenge killer on most teams.
Gourgeist Super- Being a less mixed and less bulky fur coat wall than Dusclops, it does have a niche over Dusclops in the fact that it gains a more reliable recovery in the form of leech seed, additionaly it allows it to not be crippled if the opponent switches in Tentacruel or Torkoal, impair a Chansey/Blissey switch in, and be able to cripple a Greninja with a will-o or just KO it with a seed bomb if its taken any damage (0 Atk Gourgeist-Super Seed Bomb vs. 4 HP / 0 Def Greninja: 240-284 (83.9 - 99.3%) -- guaranteed 2HKO)
Tentacruel- With magic bounce, sp. def Tentacruel can completely wall all non-smash torkaol, but still beats special smash torkoal 1v1, and is only beat by sets carrying eq. Additionally, in can hold its own vs the most of the trapping mons due to its inability to be toxic stalled. Furthermore, it can set t-spikes(which I have found to be extremely useful in the meta), while simultaneously spinning away and reflecting other hazards.
Thundurus-T- It gets water absorb. With a scarf, it reliably can threaten Greninja with volt switch and abuse the low number of common ground types.
Lucario-M- Although at this point I'm not sure if he's part of the group of recognized powerful pokemon at this point, with Aerilate and Espeed, Lucario can come in and revenge kill non-sashed Simple bugs without any trouble whatsoever. Also, its high speed and attack allow it to make for a very good SD sweeper, although it has to choose between crunch for fur coat ghosts and and stone edge to lure and destroy wonder guard mons.
Shaymin-S- By far the best of the trpper mons, due to it having one thing that rest don't: immediately powerful special attack coupled with speed higher than even Greninja. In addition, it can use a subseed + two attacks to create a good balance between defensive and offensive trapping.
Other than these things, I can't think of anything off the top of my head that consistently can contribute to every match they are brought too, however the use of entry hazards have been extremely useful for me in most matches, as so far I haven't seen too many teams prepared to deal with them. The standard threats that have already been discussed in the thread (Greninja, Snorlax, Shadow tag, Torkoal, Deo-S, Ludicolo/ slowbro) are also, as we know, very useful. Things like Raikou, Lanturn, Ampharos, Dragalge, Skarm, Starmie, and the simple bugs I've also seen been used to good success, however they all struggle consistently against a good amount of the most used mons, however they don't consistently perform as well as other things for various reasons.