Sub Culture
Archimedean Dynasty
Syndicate American Revolt
Syndicate Wars
Overboard! (Shipwreck)
G-Police
Sub Culture and Archimedean Dynasty are easily the two best underwater/submarine simulation games ever. Sub Culture being effectively the first PC game to use 3D hardware acceleration, truly the good old game. Both of them are RPG's in which you pilot submarines, and cruise expansions underwater environments doing missions like collecting minerals or destroying creatures.
American Revolt is the expansion to Syndicate, which GOG recently released and is quite popular round here, so that's a no-brainer. And we all remember Syndicate Wars, the sequel.
Overboard and G-Police are made by the same company, but very different games. Overboard is a fun little game where you cruise around in a pirate ship, high look-down camera mode, shooting canon balls at other ships, etc. G-Police is a futuristic flyer simulation, you pilot a helicopter-like hover aircraft fighting crime.
I would pay to see these titles on GOG, very good games.