Here is one which would actually run under Linux. It claims to work with any emulator, so I would guess that each option in the menu launches a script or an application with particular arguments. Might be more what you're looking for.
BTW this is just one result from a Google search for "linux launcher joystick". There might be more, or ones which are better.
Edit - just tried the Windows version of that app (couldn't be bothered to compile it...) and it looks pretty good. Very configurable, and launch anything, so no problems getting it to launch UAE with a specific config. I couldn't test it with a joystick as I don't have one, and I don't know if it will compile under PS3 Linux. But it's a start ;-)
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moto