mupen64plus with arcade joystick, fightstick, or fightpad

Edit mupen64plus.cfg, set the controller config to 0 (manual) and then set X and Y axis like so:

X Axis = "hat(0 Left Right)"
Y Axis = "hat(0 Up Down)"

Full fightstick configuration:

[Input-SDL-Control1]

# Mupen64Plus SDL Input Plugin config parameter version number.  Please don't change this version number.
version = 2
# Controller configuration mode: 0=Fully Manual, 1=Auto with named SDL Device, 2=Fully automatic
mode = 0
# Specifies which joystick is bound to this controller: -1=No joystick, 0 or more= SDL Joystick number
device = 0
# SDL joystick name (or Keyboard)
name = "Hori SOULCALIBUR V Stick"
# Specifies whether this controller is 'plugged in' to the simulated N64
plugged = True
# Specifies which type of expansion pak is in the controller: 1=None, 2=Mem pak, 5=Rumble pak
plugin = 2
# If True, then mouse buttons may be used with this controller
mouse = False
# Scaling factor for mouse movements.  For X, Y axes.
MouseSensitivity = "2.00,2.00"
# The minimum absolute value of the SDL analog joystick axis to move the N64 controller axis value from 0.  For X, Y axes.
AnalogDeadzone = "4096,4096"
# An absolute value of the SDL joystick axis >= AnalogPeak will saturate the N64 controller axis value (at 80).  For X, Y axes. For each axis, this must be greater than the corresponding AnalogDeadzone value
AnalogPeak = "32768,32768"
# Digital button configuration mappings
Start = "button(9)"
Z Trig = "button(3)"
B Button = "button(2)"
A Button = "button(6)"
C Button R = ""
C Button L = ""
C Button D = "button(0)"
C Button U = "button(1)"
R Trig = "button(7)"
L Trig = "button(4)"
Mempak switch = ""
Rumblepak switch = ""
X Axis = "hat(0 Left Right)"
Y Axis = "hat(0 Up Down)"