I love X3: Terran Conflict. Really well thought out game, plenty of stuff to do in terms of missions as well as plenty of sandbox, loads of different ships and weaponry, plenty of trading and building your own space stations/factory complexes, combat and exploration.
The initial learning curve is almost vertical mind you so be prepared to be baffled and frustrated at first (and looking for tutorials on youtube!), but it's a very rewarding game once you learn the basics.
Edit to add: The combat in X3:TC is 'proper' with you in control, you can use joystick for exploration and combat and keyboard/mouse for trading and building and menu navigation if you wish. The game also has built in multi-monitor support, so you can easily have the view from your ship on one monitor and maps/menus etc. on another, if you have more than one monitor. It's not necessary though, that's just the cherry on top - you won't be hampered by just using a joystick (or kb+m) and one monitor. And you can also build up a fleet, have them on carriers or fly behind you, and command them into action alongside you for large battles - in that way it manages to combine being in the thick of the action in your own ship, with the tactics of engaging in large multi-ship battles and commanding a fleet - and you can choose to be piloting any of the ships that you own, from the smallest fighter/scout ship, to a large destroyer. It really is a superb game, if you're prepared to sink in a bit of time to learn it.