I've been able to successfully play 3 player Rampage & Rampage 2 (though both are choppy) with 3 sixaxis controllers. Configuration is a snap. Just configure the 1st controller as you like it ([controller 0]) and then copy and paste the mapping from that one over each of the other ones ([controller 1] through [controller 3]). Here are some additional pointers about controller mappings that may or may not be obvious:
* Backup your original configuration--it's very useful as a reference if you already have some things mapped the way you like it.
* Controller should be marked as plugged in (aka plugged=1)
* The mouse input should be off (aka mouse=0) unless you are configuring keyboard input (see details below on keyboard mappings)
* Change the "device" setting for each controller mapping properly ([controller 0] gets device=0, [controller 1] gets device=1, etc).
* Don't map keyboard keys yet (since you are going to copy the same mappings to each controller section). They should all be set to 0.
* When mapping joystick buttons, keep in mind that the blight button mappings are indexed starting at 0 as opposed to the sixaxis configuration button mappings indexed starting at 1.

Once you have your configuration set just how you like it, back it up! For example, I've copied mine to blight_input.conf.p1joystick.

At this point, if you want to also support keyboard mappings, now is a good time to start tweaking that. Here are some pointers for that:
* Having mouse input enabled (aka mouse=1) allows you to use the sixaxis controller joystick (though I understand it makes control-backspace not function correctly). This setting along with sixaxis button to key mapping functionality allows you to setup your config to work with both the keyboard and sixaxis controller simultaneously pretty well.
* Change the "device" setting for only the 1st porfile ([controller 0]) to keyboard (aka device=keyboard).

Like the controller-based config you already did, once you have your keyboard configuration set just how you like it, back it up! For example, I've copied mine to blight_input.conf.p1keyboard.

Other than the obvious benefits of having your configurations backed up, you also now have the ability to switch between the two easily (either by xterm, power button configs, queen bee widget, etc). I personally just do it the old fashion way using xterm made easier by adding the following to user's .profile script:

Oh, also keep in mind that if you opt for the sixaxis w/keyboard input style of configuration, be sure that
keys you map don't conflict with other mupen64plus keys. For example, my L2 button is mapped to 'q'
which by default will quit/stop the n64 rom emulation. Rather than change my sixaxis key mapping, I decided
to simply change the "Kbd Mapping Stop" key in the mupen64plus.conf file.

Hope this helps!