With that in mind, let's look at the best destructions of Atlantis in Doctor Who!
The Underwater Menace
The Atlanteans employ Professor Zaroff to raise Atlantis once more. Unfortunately Zaroff is completely insane and wants to blow up the entire world. His scenes are stopped, but the city of Atlantis is flooded. Also there are fish people.
This destruction of Atlantis is good becuase you get double the bang for your buck. We see that Atlantis was sunk in the past but also get to watch it flood in the present day, a must for all Atlantis fans (or would be if the BBC hadn't lost the final episode where it floods).
Azal has been secretly manipulating Earth for millennia, viewing the planet as an experiment. He threatens destruction upon all, pointing out what he did to his last failed experiment - Atlantis! We don't know if he used some sort of laser ray or just turned up and started kicking down buildings with his giant cloven hooves, but yes, it turns out that Satan was behind it all along!
It is unclear if there were any fish people.
The Time Monster
The Doctor battles the Master through time, ending up in Atlantis in 1500 BC where the Master releases the chronovore Kronos. Atlantis is destroyed, not by flood or hairy Stephen Thorne, but by a man covered in foam padding with a lampshade on his head, flapping about on wires and squawking.
There were no fish people. Though there was a half-naked David Prowse with a bull's head.
Sadly, Atlantis hasn't yet reappeared in Doctor Who for another go at being destroyed. This is just another of lazy Stephen Moffat's crimes, as he is too selfish to blow up Atlantis and instead wants to write 'new' and 'original' things. My hope is that Atlantis will rise again once more (only to quickly sink again, of course).