Here are some shooters linked to the water element in one way or the other.
Aqua Jack (TAITO) Arcade Rail shooter with a speed boat
Darius Series (Arcade/Various Consoles & computers) you take on huge Mecha fish & various other weird mechanized, oceanic creatures.
Gynoug (1991) The 2nd stage takes place almost entirely underwater, while fighting against various obscure sea vermins.
Hydra (ATARI) another Arcade / AMIGA / Atari Lynx, Rail shooter with a speed boat
In The Hunt (1993)(PSX/Saturn/Arcades) Impressive Submarine shooter with huge end level Bosses. Some of the levels are a sunken city, an under water assault at the polar ice caps, a vertical ascent while being chased by an Ekatondahir / Titan & a visit at the tectonic continental plates)
Mega Blast (TAITO)(Arcade) The 1st level takes place under water.
Polaris (1980) A primitive Submarine shoot’em up, emulated in MAME)
Sauro (1987)( Tecfri) A sub horizontal shooter
Sub Hunter (1977) Ancient Arcade Sub shooter from TAITO
SWIV (1991)(AMIGA) Technically Not a boat game, but your jeep does turn into a speed boat for respectable amount of time at some point in the game.
Thunder Force Series – There are at least 3 stages that take place under water.
Here are all the Sub / Boat shooters available in MAME:
http://www.mameworld.net/maws/
Battle of Atlantis
Battle Shark
Destroyer
Dodgem
Fire One
HeliFire
In The Hunt
Invinco / Deep Scan
Mariner
Navarone
Polaris
Sauro
Sea Wolf
Sea Wolf II
Subs
Subroc3D
Tomahawk 777
The Deep
Wolf Pack
And then there are also some unknown PC submarine shooters:
http://www.fantasiegames.de/Games-Downl ... mes-07.htm
http://knctccc.at.infoseek.co.jp/work/submarine/