Kinda like the ships presets... if I accidently open the client with my joysticks not plugged in it sets it back to the defualts. Then I have spend 10 minutes setting up all the controls. All I would want is 2...one for joysticks and one for keyboard. Would this be hard to do? Maybe one you can set as default and the other one a back-up?

While it may not solve your problem entirely, you -can- create a sort of joystick config file to ease resetting your settings.

1. Create joySet.cfg, or something notable.

2. Fill it in something like so(Using bits of my joystick setting to demonstrate):
bind Joy0Button1 +shoot1
bind Joy0Button2 +shoot2
...
bind Joy0Pov0Up +strafeup
bind Joy0Pov0Left +strafeleft
...
{Take note that I'm not sure this following bit will work, but it's worth a try. All this can be found in your config.ini.}
set JOYX Roll
set xaxisinvert 0
set xaxiscenter 0
set xaxismindeadzone -10
...
set JOYY Pitch
...

{Keep in mind the set <var> <val> may be case sensitive.}

3. Call(and test!) your joySet.cfg by calling it ingame by entering /load joySet.cfg (if in your VO directory) or /load $Path$/joySet.cfg(Where $Path$ is the pathname to the location you stored joySet.cfg)

You could also make a handy alias, like so:
/alias RestoreStick "load joySet.cfg"
where you call it by just using /RestoreStick

yaar, exactly... I take *every* single change I make to the default wgaf.cfg and copy it out into custom1.cfg, custom2.cfg.... not only is it easier to use /load to experiment with new aliases and binds, I'd gotten used to some client updates recommending total rebuilding of config files; them's were the bad ol' days, eh?