Many of the controls in-game may be modified. Check out the manual for an overview of the initial key setting.
W, A, S, and D are used for straffing, moving either up, left, down, or right respectively in addition to the direction one is moving with one's primary drive. The speed of the ship can be decreased with Z or increased with X. One can change the direction the ship is pointing (and so also the direction the main drive is pushing one in) by using the arrow keys on the keyboard. This is fine for simply navigating around a system, but fighter combat usually requires better control and for that the mouse is probably best used. Simply right click with no menus open and that will toggle mouse control of your ship on or off.
The default targeting controls in X3:Reunion may not be optimum for most players. I have found it to be very useful to assign the "Target next enemy" to mouse wheel up and "Target previous enemy" to mouse wheel down.
Targeting enemies, neutral ships and stations, and friendly ships and stations is relatively easy. It can be very tough to target asteroids, though. The largest asteroids which can be mined can be targeted through the sector map (press .). But for the smallest, the only way I've found to intentionally target them is by deselecting one's current target (press t), at which point whatever object is nearest the target (middle of screen) will be selected if it's close enough. Even this system doesn't work too well and one seems to need to be quite close in order to target them. This helps a great deal with mobile mining and scanning the smaller asteroids for valuable minerals.