The majority of starship sims only provide tiny to small sized ships for players to pilot.  Others like StarTrek pair you up against equally big ships so any semblance of size goes right out the window.

Not too many decent starship (or ship) simulators these days. However, I've always been a fan of the Space Rangers series, check out Space Rangers: Reboot on Impulse if you want a really good turn based space RPG game. I wish they'd make a sequel...

How about Vendetta online?

I've been playing a ship battle game that is of some interest - Battlestations Pacific and Battlestations Midway. The controls are fairly pleasant, you can switch from capital ship to fighters to subs and even land bases. All the different ships - crusiers, destroyers, battleships - each has their role, and you have real old fashioned torpedo bombers and everything.

Battlestations Pacific in particular is too arkady to be called a simulator though, and the multiplayer battles are FAR too similar to World In Conflict or just a FPS team deathmatch. However, the game works. Something similar in space would be nice.

As for what's out there .. from what i can tell, everything worth mentioning has allready been mentioned.

Perhaps a special mention should go to Star Trek Online - you do have a bridge crew and so on, but it really is not what the OP was looking out for, even if the ship battles are pretty good... the whole 'Use phasers to take down the shields then punch torpedoes in the hole' thing works pretty well.

Jutland does sound interesting... I may have to give that a look.

(As does shatterstar and star vega.).

Probably already mentioned, but Naumachia sounds like it is going to be BP in space.  Unfortunately, it seems to be in a development purgatory at the moment. 

If I can make one contribution to you all as gamers, it would be to play Nexus: The Jupiter Incident. After patches the game went from buggy hell to a playable game, and while the story is fairly typical with a few twists, the gameplay is truly top-notch and I would kill for the system to be used again. It answers the question of the "I still have to pilot the ship" by forcing you to manage weapon systems, ordering crewmen to regulate power levels, choosing which weapon systems to target on the enemy ship, and many other options that allow you to feel less like the navigator on a ship and more like the arm-chair captain of our own space ships. The game eventually comes down to small fleets, each that can be AI commanded and you giving general directions to direct control of their systems as well. In many ways, it allows you to follow through with many a space captain fantasies. Should you send marines over to sabotage the ships weapon systems, send fighters out to intercept their bombers, or divert power from the shields to use your last ditch super-weapon. While the game seemed to kill the company that developed it, and it is by no means a perfect game, I cannot stress enough how much I loved the game, and for 10 dollars at most places, it is a wonderful game indeed.

Apply the current patch and all copy protection is gone. (applies to both Reunion and TC)

TC uses the exact same system so all Reunion mods can be (and pretty much have been) converted to TC with minor alterations. TC has better support for user created "stuff".
Capital ships work a lot better in TC than they did in Reunion because they had a lot of model/turret related issues back then.

The big thing about the X games are the mods and scripts. They have functionality that you couldn't even dream of in other games.
How about customiseable coordination for a carrier fleet complete with "learning" crew, recon wings, and supply tenders?

Now the game I want back is Taskforce 1942. Even with the old graphics.
I think I had that on 5.25" floppies.

Only thing I dont like about the X seires is how captial ships are controled...  If it would give me a nice Captial ship control  where I could Set banks of weapons for Use..      I think captial ships would be controled more like a simulation,  With your ship in the center of the screen, where you could Click + sift to set a point for you ship to head to, and Break weapons in to banks... I would be happy... Just dose not feel right trying to control a captial ship like its a fighter...

And Where is My Freespace 3.........   T,T Thats one series I really miss..   

You can already click on a point on the sector map and your ship will go there on autopilot.

Weapon loadouts can be assigned via hotkeys and there are quite a few turret scripts to choose from.
There are tons of scripts to do all kinds of such things.

Yea but that dose not give you Z axis control...  Wich is important in a tactical ingagement...    Kind of liks Starshatter   Lol I like the 2 360 compass wheels... One for X, and one for Z ... Just feels more Captial shipish..

When you tilt the sector map, you can give that order on the "other plane" but it's obviously not an ideal system.
You can give an AP order to go to a defined point in 3D space, though.

It's still largely pointless because X3 battles are fought practically at knife range and are quick.
And you really don't need the Z axis often. The sectors in this game are pretty flat.
Games like Taskforce 1942 had more of a battleship feeling where you would walk the artillery towards the targets and adjust your fleet's courses.

You guys want a starship simulator, you've got it:

Shores of Hazeron

Every other starship simulator pales in comparison.

 im looking too for a starship simulator

Looks like we got our first title!

Artemis Bridge Simulator

Here's a vid:

http://www.youtube.com/watch?v=AnZszGvpTrQ&feature=player_embedded

I really like the potential here!  Of course, I won't be happy until there is a single player mode (with PvP over the internet), but it certainly is a step in the right direction!

Pretty cool Freespace Open trailer

http://www.youtube.com/watch?v=xhAR8rWPluQ

No idea what state the project is in, but worth checking out the trailer at any rate.