Magnezone is probably the prime Pokémon to slaughter Skarmory, it has all the equipment.
A Thunderbolt coming from a base 130 Special Attack Pokémon will almost always land a OHKO on the standard Skarmory. Magnezone also resists both of Skarmory's STAB, although attacks from Skarmory aren't much of a worry in the first place.
The thing that sets it apart from other Skarmory counters is its Ability Magnet Pull, which traps opposing Steel types from switching out. This means your opponent will be wary of even switching Skarmory in when Magnezone is still alive, and will always be on his/her toes predicting the Magnezone switch when Skarmory is in, which doesn't allow Skarmory to do much.
It's so easy to trap Skarmory, and then he's out of the game.
Although Heatran doesn't have the nifty Magnet Pull, it is also a great counter to Skarmory, with a high Special Attack and powerful Fire STAB, Skarmory usually has no other choice but to switch.
These are just a couple of examples, but good counters to Skarmory are just good Special Attackers in general, along with Taunt users that shut Skarmory down completely.