I've got a (cheap) Logic3 USB Playstation style gamepad, but in games
like Defender I can move the ship up, down and left and right but can't
  fire, although it's fine in Frogger :)

The pad configuration is like this:

Buttons on left pad (clockwise from top) 1,2,3,4

L1 - 5
R1 - 6
L2 - 7
R2 - 8

SELECT - 9
START  - 10

Also with three buttons above SELECT/START - MACRO, MODE AND TURBO
(Pressing MACRO just seems to light up a red LED, the other two seem to
do nothing)

Alas using option and Command don't seem to work when the joystick
option is selected. Is anyone having more luck with their USB gamepad?