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Rotom-A is the perfect counter to Metagross. Rotom-A resists all of Metagross's main attacking options while also being immune to Explosion and Earthquake. Rotom-A can immediately threaten Metagross with Will-O-Wisp, who obviously won't enjoy being burned, or stall through Rest + Sleep Talk if needed. Rotom-H can also severely weaken Metagross with Overheat; in fact, minimum Special Attack Rotom-H stands a small chance of 2HKOing Metagross with Overheat, provided Metagross has taken previous damage from Stealth Rock. Zapdos is also immune to Earthquake, resists Meteor Mash, and can severely damper Metagross with Heat Wave.
Skarmory can come in on most of Metagross's attacks with ease. Choice Band ThunderPunch hurts, as does Hidden Power Fire. Otherwise Skarmory can get in safely, set up Spikes, and Whirlwind Metagross away. Bronzong handles most attacks with ease as well, and unlike Skarmory, it can hurt Metagross directly with Earthquake. Forretress also does well if it has Earthquake, but out of this group, it has the most to fear from Hidden Power Fire. It won't enjoy repeatedly switching into Choice Band Earthquakes, either.
Sturdy Ground-types such as Gliscor and Hippowdon can handle Metagross's attacks, but beware of Attack boosts when switching into Meteor Mash, particularly from the Choice Band set. Swampert is less at risk from boosts as it resists Steel. For Hippowdon, and especially Swampert, beware of Grass Knot. Gliscor should be careful not to get hit with Ice Punch.
In general, most bulky waters can easily wall Metagross that do not carry ThunderPunch, but one has to be wary of Explosion. Suicune, Vaporeon, and Slowbro are the most notable bulky waters that can switch into Metagross, primarily because they have the ability to recover off any damage Metagross might induce upon them. Suicune and Slowbro can easily Calm Mind if the opponent is foolish enough to stay in.
Magnezone terrorizes any kind of Metagross that cannot Earthquake it before it uses Magnet Rise. Magnet Pull prevents Metagross from running, so if Magnezone is faster and Metagross is low enough on HP to be OHKOed, Metagross is a goner. Should Metagross be locked into any attack besides Earthquake or Hammer Arm, Magnezone will also come out on top. Dugtrio can also trap and kill, but can't switch in directly on an attack that isn't ThunderPunch.
For the most part, keep Metagross away from Fire-type Pokémon if it isn't carrying Occa Berry. The vast majority will die to a well predicted Earthquake, although Charizard's and Moltres's immunity to Ground attacks means they can usually get in safely and force Metagross out. Beware of ThunderPunch and the rare Rock Slide, and switching in when Stealth Rock is on the field will also be problematic.
In Uber battles, Groudon, Kyogre, and Palkia are fine counters. Ho-Oh works in much the same way as Moltres and Charizard. Lugia can also set up a Reflect while Metagross is out and recover off any damage.
http://www.smogon.com/dp/pokemon/metagross
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