The ones I can think of are:
Last Resort (NEOGEO) - Another bearish & dark themed shooter with many references to a post-apocalyptic world.
Very pessimistic indeed.
Metal Black - The 1st level takes place in a remote desert waste-land that has swallowed a destroyed city from the ancient world.
The wreckage scattered around, the Aircraft-carrier that gets carried away on the back of a huge mutated crab and the whole devastated scene, definitely refers to a majorly ravaged world.
Ikaruga - The whole dark & sinister theme of the levels and enemies indicate a world that has just recovered from a destruction of global scale.
R-Type Delta – Level 1 – Another devastated city and a battle taking place in the surroundings as the Bydo forces besiege the city.
R-Type Final – Level 1 - Metropolis Quietus: a glass domed city of gigantic proportions lies in ruins. It looks more like a futuristic space station that has crashed into the sea.
Level 3 - Battle ship raid and the scourged city being bombarded by the battle cruiser.
Radiant Silvergun (Obviously)
Raiden I – The 1st stage is full of craters & wreckage and towards the end (Just before the Boss Fight) you fly over the huge wreck of a crash-landed battle cruiser.
Raiden II – 1st stage, again similar craters and wrecks but only larger this time round indicating greater devastation. There is a large crater on a mountain next to a bridge, which has actually flooded from a near by river!
RayStorm – Most of earth’s surface was heavily bombarded and destroyed by the Sicilian Allies’ fleet.
As a result, in the a green battle map of Europe shown after the completion of each stage, a large portion of France and the surrounding countries, is completely wiped out from the map, leaving a huge crater flooded in water. That is where the 2nd level takes place.
(I hope our folks here from Netherlands, Belgium, Luxemburg & France, all survived the Blast!
Thunder Force V (PS-1) - “In the first battle against the Guardian's weapons, created with
Vasteel Technology, humanity suffered a crushing defeat”.
Most of the earth’s cities were completely wiped out, by the Judgement Fleet’s nuclear-beams from orbit, leaving no hope for the surviving human race.
The intro sequence leaves no doubts about that.
It can’t get any worse than this!
List all that you can think of and some detailed description.

