I'd say the biggest troubles would be Rotom Wash, Scrafty, and Gengar, for me anyway. They aren't that tough, but can be tricky to play around.
Rotom is tricky because its generally bulky, making it hard to kill without hitting it for super effective damage, but its only weakness is grass. Add that to the fact that it can Will o' Wisp physical attackers and trick defensive Pokemon means the only really good counter for it is a special attacking grass type, which there aren't too many of. Thankfully, its only recovery move is pain split. With recover, it would be really annoying. Without, it's not that tough.
Scrafty can really sweep unprepared teams. His STABs let him get nearly unresisted coverage, Drain Punch makes him a pain to beat in a stall war, and the fact he has only 2 weaknesses (one of which nobody ever uses) makes him tricky to take out. After a few Bulk Ups he can take hits from even fighting types while recovering most of the damage back with Drain Punch, and after 2 dragon dances he outspeeds pretty much everything. His overall bulk is annoying, too.
The last is Gengar. I don't know why this thing isn't used more, but I'm glad it isn't. In a metagame revolving around speed, this thing's impressive base 110 speed is truly great, although it barely fails to speed tie thunderus, which can be a problem. Still, there are pretty much no surefire counters to Gengar. His overall impressive attacking movepool lets him hit a lot of stuff super-effectively, pain split and substitute allow him to beat general special walls like Blissey and Chansey, and Psychic and Disable make him difficult to beat with bulky fighing like Conkeldurr and Machamp using Payback. With his immunity to fighting and ground he can easily switch in on attacks. The only thing that hinders him is 4-moveslot syndrome. Without Pain Split, it has trouble dealing with Blissey or Chansey. Without Disable or Psychic it has trouble with Machamp and Conkledurr. Without Focus Blast it has trouble with steels. However, I think its crazy that several spots on your team must be devoted to countering Gengar since you can't tell what moves it might have.