The VGChartz list of the best co-op games for every system ever.

[masschamber]

I already covered a whole lot of the co-op neo geo games so they should be added

Behind the Back Shooter

Nam '75, tough as nails but a good time none the less, full voice over with a descent main voice actor

Horiontal Shooters
Blazing Star Pretty pre-rendered, cool bosses, great music
Prehistoric Isle, easy to play, fun to look at horizontal shooters with pre-rendered dinosaurs
Andro Dunos, cool weapon system, though it is probably the ugliest neo geo game
Last Resort, high action horizontal shooters

Isometric Shooter
View Point, someone had the bright idea that co-op shouldn't be the default setting in this one, turn it on in the soft dip screen

Over head shooters
Shock Troopers 1 and 2, over head run and guns, multiple paths and a lot of characters
Ninja Commando, on foot shooter with ninjas scrolling

Platformers
Top Hunter Line swapping, special moves, some good boss fights
Spin master, high action platformer, lots of weapons,


Run and Guns
Metal Slug 1-3 and x, obviously, 4 and 5 aren't nearly as good
Cyber-Lip, called the poor man's metal slug, for a reason but it is an okay game

Beat-em ups
Sengoku 3, probably the best beat'em up ever, 6 different characters each with their own special moves, a deep and interesting combo system, and it is the best looking beat em up on the system, stay away from all other neo geo beat em ups, they are all ugly clunky and dull, except maybe sengoku 2, maybe

Bubble Bobble-ish games
Zupapa nice cartoony game
Nightmare in the dark, Halloween bubble bobble like game

Vertical Shooters

Ghost Pilots world war 2 shoot'em up, unlike the 194x games it is set over Germany instead of the Pacific, limited power up system, but still good,
Aero Fighters (sonic wings) 2, somewhat silly shooter (pilots include a Dolphin, a Baby, A J-pop singer, a Ninja, a goofy robot, and a Rich girl with her Nanny), great levels and Bosses
aero fighters (sonic wings) 3, much like the second one, but the structure isn't as good
Stikers 1945 x, easier and pretty over head shoot'em up,

Sports
Baseball stars 2, fast action, great animation,
super baseball 2020, power ups, goofy robots, good animation, modified foul and home run zones reduce foul balls and home runs
Street hoop, Arcade style basketball
Neo-turf masters, metal slug people make a golf game!

Wrestling,
King of the monsters, use a godzilla clone to beat up a king kong clone!

Others
Crossed Swords, sword fighting, leveling up


Since I'm probably one of the few with a jag on these boards I'll also list the co-op jag games.....
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Raiden, ...
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oh yeah and total carnage (song bird release)

and a comprehensive list of great co-op games is a great idea