This depends on how you play, but not much.
First of all: You won't need most of the controls. Some are quite handy though.
Important keys (QUERTY layout):
Ctrl = Fire weapons
Space = Fire missile
, = previous gun
. = next gun
/ = cycle through missiles (actually I'm not sure if this is "/", it is the key next to the ".")
Q = equalize shields
C = communication
Tab = afterburner
T = cycle targets
K = cycle subsystems
Y = target ship in reticle
X = countermeasure
B = targets the next bomber or torpedo
E = cycles through your "escort list" (list of important ships, enemy or friendly)
The Autopilot which is "Alt-A" instead of just "A"
The energy management is on the keys del,insert,pageup,pagedwn,home,end, its layout on the keyboard is the same as on the screen.
I don't remember the keys for speed settings since I don't use them, sorry.
I also don't remember the "glide" key, but I have it on my stick. It is most useful when flying an Arrow or Excalibur. Use it!
"next attacking ship" may also be useful.
If you use a joystick you have to assign your throttle axis to "throttle (absolute)" and maybe also your rudders.
I also have Fire1, Fire2, Tab, Y, T, X, Q, Glide on my stick.
The rest is bonus. There is some nice stuff in it (for example attacker of target which is cool in escort missions) but the keys I mentioned should be sufficient for most missions.
You can change them, except the Alt-A I think, which had to be hardcoded in the mission files IIRC.