Arcade games that have "vertical arcade modes" (I intentionally avoided most games from before the 90's):

1941
1942
1943
1943 KAI
19XX: War Against Destiny
Air Duel
Air Gallet
Ashura Blaster
Batrider (Armed Police Batrider)
Batsugun
Battle Bakraid
Battle Garegga
Bells & Whistles
Blue Hawk
Brave Blade
Cybattler
Dangun Feveron
Dimahoo
DoDonPachi (DonPachi part 2)
DoDonpachi 3 - Dai-Ou-Jou
Dodonpachi II: Bee Storm
DonPachi
Dragon Blaze
Eight Forces
Esprade
Fallen Angels: Daraku Tenshi
Final Star Force
Fire Shark/Same! Same! Same! -or- Flying shark/Sky Shark/Hishou Zame -or- Twin Hawk/Daisen Pu
Galmedes
Game Paradise: Master of Shooting, The
Gekirindan/Time Travel Shootin'
Grid Seeker
Gulf Storm
Gun Bird
Gun Nail
Guwange
Hotdog Storm
Ikaruga
Kyukyo Tiger part 2/Twin cobra part 2
Layer Section/Rayforce/Gunlock(Galactic Attack for Sega Saturn)
Lightning Fighters
Macross Plus
Mazinger Z
Nebulas Ray
Paradise Team
Psyvariar
R-Shark
Raiden 2
Raiden DX'
Raiden Fighters
Raiden Fighters Jet
Raiden Fighters part 2
Red Hawk
Samurai Ace = Sengoku Ace
Sand Scorpion
Sen Jin - Guardian Storm
Sengeki Striker (Kaneko/Warashi 1997 = Shienryu 2)
Sengoku Ace = Samurai Ace
Shienryu
Shikigami no Shiro/The Castle of Shikigami
Sky Alert
Sky Smasher
Sonic Wings Limited
Space Bomber
Storm Balde
Striker 1945
Striker 1945 II
Striker 1999 (Striker 1945 3)
Thunder Dragon
Thunder Dragon 2
Trigon, Konami 1990
Turbo Force
Twin Eagle 2
U.N. Defence Force: Earth Joker
V-Five/Grid Runner Varth: Operation Thunderstorm
Vasara
Vasara 2
Vimana
Viper Phase
Wivern Wings
XII Stag
Zing Zing Zip