Lets go over the list that are the most effective shall we?
Scrappy Kangaskhan 2HKOs with Hammer Arm. And Wondertomb can't do anything against it.
Toxic Stall but that Softboiled will get annoying unless you have Heal Block. Though it shouldn't be a problem after a while. Giratina is great with this as it also has Shadow Force and Pressure to drain the PP of Wondertomb's Shadow Force and since it's faster, it will avoid damage from Wondertomb's attacks and it also has Heal Block.
Mold Breaker users negate Wonder Guard. Especially Rampardos.
Gengar can Hypnosis, Nightmare and Curse it to death. But has to hit Hypnosis before it uses Safeguard. Darkrai can do a similar thing with Dark Void, Nightmare and Bad Dreams ability.
Suicide but Destiny Bond works too.
In Gen 5, Submersion makes it a Water Type so it gains Electric and Grass Weaknesses. So you can follow it up with Hidden Power or in Octillery's case: Energy Ball.
There's others but those are the ones I can remember right now.