Well, I have serveral on the list.
As said by HoS, Breloom is problumatic, hitting the first Pokemon with Spore, Subbing up on the switch, and hitting super hard with either Focus Punch or Bullet Seed. Gliscor, Zapdos, and Skarmory can counter it decently as long as they don't eat a Spore. You must have a decent counter to Breloom on your team in todays metagame, no questions.
Serperior (Jalorda) is also problumatic. Through the fads such as Haxorus (Ononokusu) and Chandelure (Shandera), Serperior has remained throughout as a strong offensive prescence in Gen. 5 Metagame. If you let Serperior get to +4, you had better watch out. Probably the best counter is Heatran, resisting both Leaf Storm and HP Fire, but he's the only reliable counter I've found so far. Even Blissey shakes in her booties at +6 Leaf Storms.
Finally, Excadrill (Doryuuzu) is still the huge offensive prescence we speculated before Black and White were released. If he gets a SD up, you can pretty much surrender. The only reliable counters to Excadrill are Skarmory and Gliscor.