Some say it saved the 2D genre a bit in the mid nineties, when everybody was going the 3D and games like Metal Slug were a fresh air.
Retrogamer did a top 25 in their issue 43.
25. Rendering Ranger
24. Rex
23. Shinobi
22. Narc
21. RollingThunder
20. alien 3
19 Nam 1975
18. The Chaos Engine
Beautiful game, with a nice Mobile Phone version out now. It had some literary asperiations as well, as it was inspired by the Steampunk novel "The Difference Engine"
17. Sunset Riders
16. Mercs
15. Gunners Heaven, Rapid Reload
A great Gunstar Heroes inspired game, which is strangely a very unknown playstation launch game. Stuart Campbell investigated, if it was in fact by Treasure in this intriguing article.
14. Elevator action returns
13. Jet Force Gemini
12. Alien Breed
11. Smash TV
10. Midnight Resistence.
9. MDK
8. Turrican 2
7. Ikari Warriors
6. Shock Troupers
5. Metal Slug.
Maybe the most iconic run and gun. It made the Neo Geo. It still is incredibly beautiful, although why did they milk the series so much?
4. Contra 3
3. Gunstar Heroes.
Ignored at it's release, but now universally acclaimed as a masterpiece!
2. Robotron.
Strange inclusion, but just maybe, the best game ever
1. Sin and Punishment.
The title, inspired by Dostojevski, The game until recently only available in Japan, but get it, on your Nintendo 64 or in the Virtual Console!