Sonalyst Combat Simulations' Dangerous Waters, Harpoon 3, Jane's 688(I), EA's old 688, Jane's Fleet command, Silent Hunter 1&3... (can you tell I'm in the Navy?)
On the "army-er" side of the house, EA's uber-old SEAL Team, Rainbow Six (all of them except Lockdown), Falcon 3.0, and the best-ever non-Navy (as in, non-driving-ships) game ever developped or imagined by man: F-14 Fleet Defender. Ok, so it's still Navy because you fly carrier-based F-14, but it's still relatively realistic (not talking about the graphics) and exciting, and you can set it so hard you need to have watched Top Gun a gazillion times to have a clue what you're doing, or so easy you can be a Wing Commander jockey and still be able to fly around. Oh, and all the Wing Commander games were teh @we$omene$$. (Please excuse my pathetic attempt at 1337-speek)
Ok, I realize that's like, 20 games.. My top three right now would probably be Dangerous Waters, 688(I) and F-14 Fleet Defender.
I'll go cry over the 'Cats being gone, now.