Kansas City got nuked in “The Day After”.
Sydney and Hong Kong in Pacific Rim.
Boston in Stonados.
Copenhagen in Reptilicus.
Rome in 20 Million Miles to Earth.
Chicago in the ending scenes in The Blues Brothers.
San Francisco also took a beating in last year’s Pacific Rim and Star Trek Into Darkness.
So, YOU’RE the other guy who saw that movie!
(Sock puppet monster spitting cartoon acid. Good, good times. The end?) 
Deep Impact has the tsumani at the end wiping out the entire eastern seaboard, with NYC definitely getting the full message. Same thing in ‘The Day after tomorrow’, IIRC.
Rome got quite the kicking by an electrical storm in ‘The Core’.
Jurassic Park: The Lost World is the only movie that comes to mind where my hometown of San Diego takes any significant onscreen destruction.
(Of course, that’s not the greatest disaster to ever befall San Diego in film - that, of course, was the unjust firing of Ron Burgundy from the Channel 4 news team.)
As an aside, “Racoon City” is a very appropriate nick for Toronto - the “Racoon Capital of the World”. 
Does it count if the audience is laughing hysterically, because the collosal tsumani froze solid in mid-disaster? 
London gets obliterated by some kind of quasi-nuke weapon in GI Joe: Retaliation.
Come to think of it, in the first GI Joe movie, a decent chunk of Paris (including the Eifel Tower) gets eaten by nanobots.
San Fran also takes it in the chin in the 1950’s sci-fi film It Came from Beneath the Sea.
A break from Tokyo: Fukuoka, in Gamera: Guardian of the Universe.
Not a city really, but the Salton Sea and the irrigation canals it feeds really get it in The Monster that Challenged the World.
ETA: I’ve only seen the English Reptilicus. It was shot twice with the same cast, once in Danish, once in English.
No way, that is priceless! That must have burned up most of the budget, as it certainly wasn’t spent on SFX. 
The made for TV movie 10.5 had a lengthy scene where an Earthquake took care of LA, SF and Seattle. (And the rest of their F/X budget apparently).
Seattle also got it pretty good in Chronicle.
Skyline showed LA being demolished by aliens pretty thoroughly.
One city in Independence Day got wiped out by the aliens and then had a nuke detonated over it when the US tried to retaliate. Does that set the record?
London was completely obliterated in 28 weeks later.
And in * The Time Machine * (1960).
Los Angeles was devastated in * War of the Worlds. *
Chicago in * Blues Brothers? * Similar to any Jewish community in Germany on November 9, 1938. 
Presumably quite a bit worse in Terminator 3, along with numerous other cities. In T2 it was just a dream sequence.
Montreal is recognizable but unnamed in Warm Bodies and has been trashed quite a bit.
Of all the destructions of Tokyo, probably the most brutal was the attack of the Giant God Warriors in the backstory of Nausicaä of the Valley of the Wind.
New York City in Oblivion. We don’t see the destruction itself. Just the observation deck and spire of the Empire State Building sticking out of hundreds of feet of silt.
For that matter, New York in the original Planet of the Apes. Only the Statue of Liberty’s head was left recognizable.
Which makes it the opposite of Sharknado 2. 
Got one: Seoul in Yonggary.