Off hand the only one I can think of is Battlecuriser/Universal combat or Starfury

http://www.3000ad.com/

http://www.malfador.com/

Couple of more older game you may want to take a look at,are the Hyperspeed game

http://www.planetmic.com/orbit/hyperspd/hspd01.htm

You also might try FFE..as you can fly capital ship in that game...it has been updated it d3d and uses psuedo-newtonian physics, Terminus is another good one which uses Newtonian flight, but it's basically single FPS fighter combat.

Battlecruiser/Universal Combat is your best bet, however it has a really shitty flight model.. Freespace 2 is a good one.

Also any of the X games allow capital ship flight, but again the flight model is arcade.

Also Vega-strike uses a good flight model and I think they have capital ships as well, but no control of crew.

BC/UC is your best bet.

BC3K is free and can be downloaded here: http://www.fileplanet.com/section.aspx?s=49748&v=0

BCM is free and can be downloaded here: http://www.gamershell.com/download_9337.shtml

Vegastrike can be had here: http://vegastrike.sourceforge.net/getfiles/

UC is free and be downloaded here: http://www.gamershell.com/download_22610.shtml

The first I-War game nearly fit the bill,big ship,newtonian physics,but no element of

exploration.Same goes for Warhead.

http://en.wikipedia.org/wiki/I-War_(Independence_War)

http://en.wikipedia.org/wiki/Warhead_(computer_game)

Does Freespace 2 incorporate exploration? I'm thinking about doing that one next. All the commands seem daunting to me though, especially since I like to operate on a control pad. It's a couple years older than I like to usually go, but it got such good reviews I'm considering making an exception.

No, it is mission based. There is a bunch of mods for it and you might want to install the FSO (Freespace Open Project) it really enhances FS2 and there is a host of games being written against the FSO engine.

What kinds of thing does the FSO incorporate into the game?

This covers most of the info: http://en.wikipedia.org/wiki/FreeSpace_ ... de_Project

Is it something I should install even before having played through the campaign for the first time?

Freespace 2 is a mission oriented "on-the rails" type game. It isn't a free-form open-ended type game.