Naval ships is a great setting for sci-fi horror films (and games). I recommend the following: (if you haven't seen them already)
Virus (1999) - A pretty dark film about a hostile alien energy that hits the computer system of a large research ship, and then begins controlling the onboard industrial robots that start building these crude machines that turn against the crew and harvest their bodies to form a cybernetic race.
Think The Borg from Star Trek but much more violent and nasty with lots of gore and great special effects (both practical and CGI.) The Strogg from Quake is an even better example.
Deep Rising (1998) - the more lighthearted choice here both in terms of the ship (Virus takes place on a spooky research vessel while Deep Rising takes place on a luxury cruise ship) and the overall tone, which is a bit more ridiculous and exaggerated here with a tiny ounce of humor, but it's nonetheless a good film that I recommend.
It's about giant serpent-like creatures (not going to spoil the truth here :) attacking the ship and killing everyone.
What these two films have in common are the fantastic visual effects for its time.