Well, Shaymin-S holding a scarf can outspeed Groudon after a Rock Polish if Groudon isn't using a Jolly nature. Giratina-O can survive a Stone Edge and do massive damage with Draco Meteor. Scarf Mewtwo can outspeed it (as long as it isn't Jolly) after Rock Polish, and do a lot of damage with Ice Beam/ Grass Knot. Wobbuffet can usually survive any attack it has, and OHKO with Counter. A Groudon of your own can take a hit and Roar it away. A Choice Specs Kyogre with 252 HP will not die to Earthquake as long as Spikes aren't down, and can OHKO with Surf. Lastly, a Lugia can take a STone Edge and set up Reflect, then procede to Whirlwind Groudon away. There are probably more, but this, hopefully, is enough for you to choose from.
I'll add few to this list if you don't mind, as some of them are viable in Ubers ;).
For first probably the best counter is Bronzong. Resist all Groudon attacks (bar not often Fire Punch) and may Toxic Groudon or just Gyro Ball it for good damage.
Another good option is Cresselia. Just to show you Cresselia survives +4 (!) Swords Danced Stone Edge from Groudon. When you switch Cresselia on RP Groudon, then Groudon can't do anything.
Another good counter, which I personally love to use if Physically Defensive MewTwo. You switch in, Groudon attacks when you Reflect, you easily Recover and from there you may WoW/Ice Beam it to death. Also thanks to Taunt MewTwo does well against Ubers Stall.
Physically Defensive Skarmory (specially defensive also isn't bad, however critical Stone Edge hurts as hell) is another good check. You may throw spikes, Roost when neccesary and just Whirlwind poor Groudon away.
Not popular pokemon in Ubers, however Celebi is also good check for it. Grass Knot deals good damage, you resist Earthquake and may Recover any damage you have. Or just Perish Song, if you use set with this move.
I guess that's it. Firecape mention all offensive checks and that's why I didn't mention anything offensive. I hope that helps ;).