Right Trigger - Fire Primaries
Left Trigger - Fire Secondaries
Right Bumper - Switch Primaries
Left Bumper - Switch Secondaries
Left Analog Stick - Y axis flight Control, Throttle
Right Analog Stick - X/Z axis flight control
Right Analog Stick Click - Open Order Menu (I can see this being something like Dragon Age or Mass Effect, but with ship orders instead)
Left Analog Stick Click - Quick Order (context sensitive. Destroy-target for hostile non-critical ships, Disable/disarm-target for hostile critcal ships, Escort for friendly ships)
X - Deploy Countermeasure
Y - Target In Reticle (heh, funny how that one fits)
A - Afterburners
B - Target, Escort List
D-Pad Left - Switch Targets (previous)
D-Pad Right - Switch Targets (next)
D-Pad Up - Switch Targets (subsystem)
D-Pad Down - Switch Targets (turret)
Back - Call Support
Start - The obvious
Am I missing any of the really important ones? Even if I am, remember you could change something like Left Trigger into a de-facto ALT key, like in Assassin's Creed.
Also note that XBox/PS3 controllers have two sets of shoulder buttons. You forgot the triggers on this one.
EDIT: I am missing one of the important ones. Subspace Drive would probably be on the Start button Options Menu.