Name some semi-popular video game series

[Skulhedface]

Final Fantasy VI (the second half)

Final Fantasy X (Zanarkand)

Contra 3, agreed

Castlevania Dracula X (if you want to count a village on fire)

Zombies Ate My Neighbors (if you count destroying some of the buildings yourself, be it with a bazooka or Monster potion)

X-Men Vs. Street Fighter (the stage where the street breaks and yuo end up in the sewer. I believe there is a level similar to this in X-Men: CotA where the street collapses and you land on a boat)

Secret Of Evermore (this is a stretch, but if you count the other castle in the medieval world)

Final Fantasy VII (Mideel)

Alright, I'll admit, I'm being pretty liberal with "destroyed cities" here, but this is what I came up with. Hope it helps.