After a few screencaps and a mess of typing, here's the complete list of the commands useable in-game. IMHO, the Energy Management and Shield commands should be in the Ship section, but this is how they're listed in the config, except for I moved all the multiplayer only ones to their own section.
Freespace 2 Default In-Game Commands Settings.
Targeting
Target Next Ship = T
Target Previous ship = Shift-T
Target Closest Hostile Ship = H, Button 3
Toggle Auto Targeting = Alt-H
Target Next Closest Friendly Ship = Shift-F
Target Ship in Reticle = Y, Button 5
Target Target's Nearest Attacker = G
Target Last Ship to Send Transmission = Alt-Y
Turn Off Auto Targeting = Alt-T
Target Subsystem in Reticle = V
Target Next Subsystem = S
Target Previous Subsystem = Shift-S
Turn Off Auto Targeting of Subsystems = Alt-S
Target Closest Attacking Ship = R, Button 7
Target Target's Target = J
Target Next Escort Ship = E
Target Closest Repair Ship = Alt-R
Target Next Uninspected Cargo = U
Target Previous Uninspected Cargo = Shift-U
Target Newest Ship in Area = N
Target Next Live Turret = K
Target Previous Live Turret = Shift-K
Target Next Hostile Bomb or Bomber = B
Target Previous Hostile Bomb or Bomber = Shift-B
Ship
Forward Thrust = A
Reverse Thrust = Z
Bank Left = Pad 7
Bank Right = Pad 9
Pitch Forward = Pad 8
Pitch Backward = Pad 2
Turn Left = Pad 4
Turn Right = Pad 6
Set Throttle to Zero = Backspace
Set Throttle to Max = \
Set Throttle to One-Third = [
Set Throttle to Two-Thirds = ]
Increase Throttle 5 Percent = = (Equal)
Decrease Throttle 5 Percent = - (Minus)
Afterburner = Tab, Button 6
Bank When Pressed = None
Turn (Yaw) Axis = Joystick/Mouse X Axis
Pitch Axis = Joystick/Mouse Y Axis
Bank Axis = None
Absolute Throttle Axis = None
Relative Throttle Axis = None
Weapons
Fire Primary Weapon = Left Ctrl, Button 1
Fire Secondary Weapon = Spacebar, Button 2
Cycle Forward Primary Weapon = . (Period)
Cycle Backward Primary Weapon = , (Comma)
Cycle Secondary Weapon Bank = /
Cycle Secondary Weapon Firing Rate = Shift-/
Launch Countermeasure = X, Button 4
Misc
Match Target Speed = M
Toggle Auto Speed Matching = Alt-M
Attack My Target = Shift-A
Disarm My Target = Shift-Z
Disable My Target = Shift-D
Attack My Subsystem = Shift-V
Capture My Target = Shift-X
Engage Enemy = Shift-E
Form on My Wing = Shift-W
Ignore My Target = Shift=I
Protect My Target = Shift-P
Cover Me = Shift-C
Return to Base = Shift-J
Rearm Me = Shift-R
Chase View = Pad *
External View = Pad . (Decimal Point)
Toggle External Camera Lock = Pad Enter
Free Look View = Pad 0
Current Target View = Pad /
Increase View Distance = Pad +
Decrease View Distance = Pad -
Center View = Pad 5
View Up = Hat Forward
View Rear = Hat Back
View Left = Hat Left
View Right = Hat Right
Cycle Radar Range = ' (Apostrophe)
Communications Menu = C
Enter Subspace (End Mission) = Alt-J
Increase Weapon Energy = Insert
Decrease Weapon Energy = Delete
Increase Shield Energy = Home
Decrease Shield Energy = End
Increase Engine Energy = Page Up
Decrease Engine Energy = Page Down
Equalize Energy Settings = Alt-D
Equalize Shield = Q, Button 8
Augment Forward Shield = Up Arrow
Augment Rear Shield = Down Arrow
Augment Left Shield = Left Arrow
Augment Right Shield = Right Arrow
Transfer Energy Laser->Shield = Scroll Lock
Transfer Energy Shield->Laser = Shift-Scroll Lock
Add or Remove Escort = Alt-E
Clear Escort List = Alt-Shift-E
Increase Time Compression = Shift-. (Period)
Decrease Time Compression = Shift-, (Comma)
Toggle HUD Contrast = L
Multiplayer Commands
Message All = 1
Message Friendly = 2
Message Hostile = 3
Message Target = 4
Observer Zoom to Target = Alt-X
Toggle Network Info = Shift-N
Self Destruct = Shift-End