I use a Cyborg 3d joystick and a nostromo N52, with a keyboard for the less criticle commands and comm. But i've been trying to get my Nyoko PS2 styal controler set up properly. I just can't finde a configuration that matches the functionality of the joystick/N52 combo.

I use a lovely four-button-plus-mousewheel mouse and a standard keyboard. Left-click is primary fire, right-click is secondary fire, left-side click is tertiary fire, right-side click is toggle autoaim. I don't think the mousewheel does anything.
As for the keyboard... duh.
-:sigma.SB

On my mouse, the left-side thumb button is activate, left click primary fire, right click secondary fire, right-side tertiary fire (or whatever else I feel like binding it to; toggle auto-aim or toggle flight assist are other things I often have on the right-side button), and the wheel is variable zoom.

My keyboard binds are modified from the default, as well, most notably w is strafe up, s strafe down, r forward thrust & f reverse thrust.

Finally found a good set up for my saitek x45 . . .

The X and Y axis are used for straffing; trigger is set to primary fire; finger lock is set to secondary fire; safe button is set to tertiary fire; buttons A and B set to weapon groups 1 and 2 respectively; Fire C button is slotted for auto destruct; lower thumb pad is used for forward and reverse thrust; and upper thumb pad is used for targeting and braking.

My mouse is set for pivoting. Left and right mouse buttons for rotating; and middle mouse button is slotted for turbo.

Tried to use the zoom bind in the bind section for the mouse wheel but I couldnt get it to work. Tried it three times . . . only thing I could get was one zoom out of it.

I havent played much with the companion slider controller. Once I get used to using a joystick I may move away from the mouse altogether and try both controllers together.

I use my trusty old gravis firebird 2:
http://www.ixbt.com/peripheral/images/firebird2.gif

The group of six buttons on the base are mapped to strafing and rolling the 3 above are jump boost "player in sector"
the hat buttons are:
up/down = forward/backwards
left/right = roll
the rest of the buttons on the stick are "target nearest enemy" "target infront" primary secondary

another button for the teriary group would be nice but you can't everything :P

It's a bit like playing with keyboard and joystick this way ... just less clumsy.

The only real bad things about this stick are that it's a bit wobbly, the buttons are a bit smallish, and the calibration is never quite right.
Oh and it's starting to show signs of of age. The buttons aren'T quite as responsive as they used to be anymore :D