Crusader Scott: I too was looking for what you are looking for. I can recommend Klingon Academy if you can get it. I managed to get a full version sent to me by a mate on a forum like this.
Here are some newer games that do "space combat simulation"
Starshatter: the gathering storm
This game is amazing and lets you command squadrons of capital ships or fly fighters all in a dynamic campaign or even coop missions if you wish. I highly recommend it. The latest iteration only came out a year or two ago. The Battlestar Galactica mod is simply amazing if u like commanding battlestars and flying viper fighters.
You get to choose what your starships target, what alert status your fighters go to, how they patrol, how damage control is taken care of, what weapons to use etc
Nexus: The Jupiter Incident:
Another classic that still looks awesome graphically. It again allows you to command cap ships, target enemy subsystems/damage control etc
EVE: This game is junk. Its just an excuse for stats chasing and gear collecting in space. Exactly the same as WOW.
I thought this game looked good but played like Freelancer. Not a starship sim but a trading "compulsive collecting/level up game
Angels Fall First: The Second Antarean War
MMORTS BETA2 jan 11 Dunno how this will turn out but looks interesting.
Love to know what u think of my suggestions
Also if you want a real starship simulator "like a NASA grade one" try orbitor. My friends have taken this real physics sim into geosynchronis orbit and then slingshoted to land on Venus and stuff like that.
P.S. A real life ship fleet simulator I am playing at the moment (ww1 naval) is called Jutland.
BONUS: Babylon 5 I've found her - real newtonian physics in a space fighter campaign