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I am going to start Pokémon Showdown! in a few weeks, and I want to plan out my team in advance. I consider myself to have decent knowledge of competitive play already, but I still have a lot to learn. I need to know the top/most common threats in each tier, and preferably how to counter them. I already know Talonflame (everyone who's anyone knows about Talonflame), and I know that Greninja is undergiong a suspect test for Ubers. But aside from that, I have only general knowledge about "what is a good counter for this Pokémon?" kind of stuff. Any help will be appreciated!

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Check on smogon. They have threat lists. Here is an example: http://www.smogon.com/bw/articles/bw_ou_threatlist . The bad thing about this is that they aren't updated.
I looked at those, but I want a more up-to-date listing.
Yeah I agree. I'll try to find more up-to-date listings.
Here's one for X/Y OU, but it only shows the most buffed ones: http://www.smogon.com/smog/issue34/most-buffed-threats

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Best answer

I'm going to look super lazy stealing from Smogon like this, but honestly, their viability rank lists are by far the most accurate and up-to-date listings. I'll include links to the lists for each tier, and copypaste each "S" ranked Pokemon.

Note, the most up to date version can be found by clicking on the links. The ones here might be out of date!

Ubers ranks, S ranked Pokemon are:

  • Primal Groudon, who Smogon makes a point of promoting to S+. It has no Water weakness and a fantastic new move in Precipice Blades. You will see this on every second team it's that good.
  • Arceus Normal, the ExtremeSpeed user that has been known for its deadly Swords Dance set since Gen 4.
  • Ho-Oh, an incredibly versatile Pokemon with a number of viable sets and access to Sacred Fire, which has a 50% chance to burn, making Ho-Oh a difficult Pokemon for physical attackers to switch into.
  • Mega Gengar, whose ability to trap and kill Pokemon makes it well worth a Mega slot. Its presence immediately shuts down Pokemon, and it holds the title of the first Pokemon quickbanned from Gen 6 OU.
  • Mega Salamence, who is just as good in Ubers as it was in OU due to its ridiculous power and bulk that trumps even some cover legendaries.
  • Xerneas, one of the most hated Ubers Pokemon due to its effortless setup move, Geomancy which is essentially Shell Smash with no Defence drop.

OU ranks, S ranked Pokemon are:

  • Keldeo, who reclaimed its position as the best Water attacker in the tier after Greninja was banned. It has a great typing, good coverage of the tier and enough bulk to switch into attacks reliably.
  • Mega Metagross, a very scary physical attacker who is currently undergoing a suspect test. It is very bulky, very fast, very powerful and packs great coverage.
  • Mega Sableye, a fantastic stallbreaker thanks to Magic Bounce who packs a great typing and good bulk. It can run Calm Mind sets to turn passive Pokemon into setup fodder.

UU ranks, S ranked Pokemon are:

  • Salamence, who dropped to UU recently and has proven to be an extremely threatening sweeper. It is very difficult to deal with due to its power and decent bulk that prevents it from being revenge killed too easily.
  • Mega Aerodactyl, one of the fastest Pokemon in the game who can outspeed some Choice Scarf users and can move before Mega Beedril and Mega Sceptile and beat both of them. Its Hone Claws set is a very threatening sweeper.
  • Suicune, who can basically shut down an entire team very early in the game if you allow it to set up Calm Minds. CroCune is easy to use and very hard to stop. If your team can't counter this, don't bother using it.

RU ranks, S ranked Pokemon are:

  • Cresselia, who is has crazy bulk and the ability to shut down a ton of Pokemon, setting up on tons of Pokemon.
  • Pangoro, an very threatening bulky attacker who is very difficult to switch into due to the sheer power of Choice Band Knock Off.
  • Moltres, who is just as scary as ever with its ridiculously powerful STAB and wide coverage of the tier.

NU ranks, S ranked Pokemon are:

  • Mega Camerupt, who is very difficult to switch into because Sheer Force Fire Blast wrecks everything. It's also quite bulky, making hard to stop before it fires off its powerful attacks.
  • Mega Steelix, who is ridiculously bulky, has a great Attack stat and is a very difficult Pokemon to kill. Also takes advantage of the occasional Sand team.
  • Typhlosion, whose max HP Eruption leaves massive dents in even the bulkiest Pokemon in the tier.
  • Heliolisk, who dropped from RU recently and got suspect tested with Mega Steelix almost immediately. It's very fast, deals good damage and is a massive threat in general.
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This is just what I was looking for, I jus tcouldn't find the lists of their rankings.