While Hydra rarely gets to be AWESOME, it did utterly humiliate Norman Osbourne by absorbing the entirety of HAMMER into its ranks. Effectively absorbing an entire branch of SHIELD (the American one) to bolster itself.
Madame Hydra didn't get one for seducing Wolverine, that's easy enough when you're a sexy villainess, but using it as political leverage to take over a country is another matter.
Baron Strucker blowing up an entire base of Hydra agents to annihilate the Skrull infiltration of his organization.
Possibly a little excessive.
Subverted by Hank Pym rescuing the President of the United States from a massive Hydra attack. Not only was it not the real Hank Pym but the Hydra agents were probably suicidal Skrull agents.
Nick Fury taking down the entirety of Hydra Island and saving the world from the Death Spore virus.
Wolverine's revenge for his mind-control is to try and kill every Hydra goon on the planet. He almost succeeds.
Nick Fury gets his greatest one at the end of Secret Warriors. Destroying Baron Strucker completely by revealing how much a fool he'd been played before executing him.