I just bought this game, but I'm lost. I see so many control options and I don't know which ones are important and which ones I'm going to use often. Can you help me out? I also don´t understand the descriptions, I don´t know what some keys do exactly.

I have a Thrustmaster t16000m joystick, it has 16 buttons and a throttle/slider.

It is a really complex game and I know that at first it can be difficult to know which functions you will use often. I only got a joystick today, and although I already played the game with mouse and keyboard before, I was also not entirely sure how to configure the buttons. But this seems to be a good start: http://www.gog.com/forum/freespace_series/joystick_configuration

It would be best to play for a while and then decide for yourself which functions you need the most, besides these, and then you can put them on your remaining buttons, or change the layout to your desire. I find that I still use the keyboard together with the joystick, it's just a very complex game with a lot of different functions, and most of them are useful in one way or the other, if only in a few situations.