According to the PO Uber Usage Stats for this month, the Top 5 Used Uber Pokemon are Kyogre, Mewtwo, Arceus, Groudon, and Dialga. I'll only be explaining these 5, so here we go:
Kyogre is the #1 Used Uber Pokemon, due to Drizzle and its extensive Movepool. Specs+Boosted STAB Water Spout is a force that can 2HKO most of the Uber Metagame. As for counters, Chansey and Blissey with Calm Nature, Shedinja(Explained by Josh's Gravatar), Gastrodon, Ferrothorn, and Groudon. The point on Countering Kyogre is to have a Pokemon that can switch into that Water Spout. Chansey and Blissey take pitiful damage from Water Spout, and can easily recover from damage using Softboiled. Gastrodon and Shedinja are immune to Water Spout, while Shedinja walls most Kyogre, and Gastrodon Walls Scarf and Specs variants. SDef variants of Groudon can weaken Kyogre by changing the Weather, but takes too much from Water Spout still to make it a counter. Palkia can also Check Kyogre by resisting Water Spout and causing serious damage with Rain-Hyped Thunder.
Refer to the Checks and Counters, because Mewtwo's counters all depend on its Moveset, which varies in the Uber Metagame. Can't really explain it, sorry.
Arceus is mainly used as the Swords Dance+STAB Extremespeed variant, so I will only name counters for that variant. If you let Arceus set up, without counters, you just lost the match really. Arceus is countered by a Bulky Arceus, Skarmory, Giratina, and your own Arceus E-Killer. Bulky Arceus can ruin E-Killer by using Will-O-Wisp, and taking pitiful damage from their Attacks, or can phaze them out with Roar. Skarmory just Walls E-Killer, and can phaze it out with Whirlwind or set up on it. Giratina is immune to Extremespeed and Earthquake(E-Killers common moves), and can Burn Arceus to ruin it for the match, or simply Phaze it out with Roar, removing the boosts. Giratina must beware of Boosted Shadow Claw/Shadow Force, as it can OHKO it. An E-Killer of your own can counter Arceus simply, if you nab a Swords Dance boost.
Groudon is a varied Pokemon. Being able to Tank, Sweep, and Phaze, it's Counters might seem to differ, but they don't. If you let Groudon set up Rock Polish, it could wreck your Team easily. If you let it set up Substitute, it can Wall and Cripple your Team with Thunder Wave/Toxic. Counters goes as follows: Cresselia(Smogon), Variants of Arceus, Kyogre, Giratina-O, and Shaymin-S(Smogon). Cresselia is immune to Earthquake, and can ruin it with Ice Beam. It also benefits from the Sun by using Sun-Boosted Moonlight. Arceus who resist Earthquake can Wall Groudon and proceed with Will-O-Wisp to ruin it. Kyogre can change the Weather and can OHKO with STAB Water Spout or Surf even. Giratina-O is immune to Earthquake and can Burn Groudon or Phaze it away if behind a Substitute. Shaymin-S can OHKO it with Seed Flare, but with hate switching in to Sun Boosted Overheat or Fire Punch.
Dialga is too boss to describe here. Too many variants it can be, so there is no definite Answer.