Spacegame now has a mouse-based targetting system, and user configurable controls (though right now, that would involve looking up sdl keysyms and manually editing ~/.spacegame). The closest target to the mouse has brackets around it, and you click the right mouse button to target it. Seeker missiles can now be given a target.
One thing I really need to take note of soon is all the places I refer to ships by index number, and make sure that my ship/weapon removal code fixes all those indices.
But it sure is cool to make sweeping changes to gameplay in a couple hours :)