I was wondering if anyone has a better control configuration than the default with keyboard only? It seems to me like the default is all over the keyboard, is there any better?
P.S. I play Descent with keyboard only, using the numpad as movement and space/ctrl as primary/secondary. It would be great if there is a setup like that for freespace!

Are you asking for what you should set the keys to for a good all keyboard set-up or are you asking what's would be better to use than the keyboard?
I don't have a specific good keyboard key set-up as I don't think this game is well suited for a keyboard, mouse and joystick work much better with keyboard help for the ship functions like energy allocation, etc.
But as the keys are completely customizable, you can set the keys to whatever you want them to be...

Skip the keyboard completely and buy yourself a decent joystick (Logitech Extreme 3D Pro is good one for the money). This game, like most from its genre, was always intended to be played with a joystick, not just the keyboard.

I don't play with a keyboard (Literally. Joystick/throttle and voice control) however I believe you can re-assign all the keys to where you desire them.
Karl

I play Descent a lot of the time with keyboard only, and Freespace wouldn't work the same. You have way more management stuff to do... specific targeting or speed control for example, which you don't do in Descent. Just using a mouse would help you a lot.

I've always played with just a (laptop) keyboard. Don't feel like investing into a joystick/pad. Maybe if the mouse in FS worked like in Freelancer, I might use it. Hell, I would use it. But since it works with the "ship turns as long as mouse moves" mentality, I find the keyboard less straining.

dumb question.....is a controller just as good as a stand alone joystick for this game? I could never really get into using a joystick but i have a controller for all of my sports titles.

I just started playing the Freespace games this week, and I made it through Freespace 1 using the mouse and it worked ok. I know what you mean about the mouse-to-ship movement, its not ideal.
I don't suppose there's a mod or anything that would make Freespace mouse control more like Star/Freelancer?

Assuming you're using the FS Open engine, there are several mods/scripts that can help you. I just discovered them, and haven't tried to use them yet. Setup does not appear to be very straightforward, and probably requires some work. You should start by browsing those threads :
on HLP

Unfortunately not - you really need one hand free to use all of the keyboard commands, which rules out gamepads and pretty much just leaves the mouse or a joystick.
You will use dozens of key commands in each mission, including afterburner, chaff, multiple targeting functions, weapon selection and dual-fire mode, and redirection of power and shields, so even a modern controller with more than 15 buttons would have trouble.

I have always prefered keyboard when playing Freespace, its a lot more precice than joystick and mouse once you get used to it. Whatever you do, dont play with mouse, as it feels very wierd.
To make keyboard work. Just change pitch down to numpad 5 instead of 2. This way you get to steer with numpad 8,4,5,6 (as opposed to WASD) and use numpad 7 and 9 to roll. Important: always use bank left and bank right when dogfighting (numpad 4 and 6). Rolling to turn is not as precise as banking when using keyboard

Keyboard aiming can't be as precise and comfortable as mouse aiming, that's kinda elementary truth. And for that very reason everyone use mouse for aiming and direction control in shooters on PC instead of keyboard (or gamepad).

I did well enough with the keyboard & mouse. It would've been better, though, if you could modify the mouse controls to standard instead of inverted.