There's another option now with the latest beta (at least for emulated wiimotes) It requires either renaming the ROM to include some options or creating a custom definition per ROM
Here's the default mapping:
'x': 'Buttons/2', 'b': 'Buttons/A',
'y': 'Buttons/1', 'a': 'Buttons/B',
'pageup': 'Buttons/-', 'pagedown': 'Buttons/+',
'up': 'D-Pad/Up', 'down': 'D-Pad/Down', 'left': 'D-Pad/Left', 'right': 'D-Pad/Right',
'joystick1up': 'IR/Up', 'joystick1left': 'IR/Left',
'joystick2up': 'Tilt/Forward', 'joystick2left': 'Tilt/Left'
You can add .side. to make the ROM treat your controller as a sideways wiimote
It then makes the buttons the following:
'x': 'Buttons/b', 'b': 'Buttons/2',
'y': 'Buttons/a', 'a': 'Buttons/1'
There's also 2 letter combinations (is si / it ti / in ni / st ts / sn ns / tn nt)
The first one controls the left stick, the second one controls the right stick.
i = IR
s = Swing
n = Nunchuk
If you use nunchuk settings, it also makes
'l2' = 'Nunchuk/Buttons/C'
'r2' = 'Nunchuk/Buttons/Z'
Also in the configuration is .cc. which turns your controller into a classic controller for games that support it
'x' = 'Classic/Buttons/X'
'y' = 'Classic/Buttons/Y'
'b' = 'Classic/Buttons/B'
'a' = 'Classic/Buttons/A'
'select' = 'Classic/Buttons/-'
'start' = 'Classic/Buttons/+'
'pageup' = 'Classic/Triggers/L'
'pagedown' = 'Classic/Triggers/R'
'l2' = 'Classic/Buttons/ZL'
'r2' = 'Classic/Buttons/ZR'
'up' = 'Classic/D-Pad/Up'
'down' = 'Classic/D-Pad/Down'
'left' = 'Classic/D-Pad/Left'
'right' = 'Classic/D-Pad/Right'
'joystick1up' = 'Classic/Left Stick/Up'
'joystick1left' = 'Classic/Left Stick/Left'
'joystick2up' = 'Classic/Right Stick/Up'
'joystick2left' = 'Classic/Right Stick/Left'
And then the big change is the ability to define a custom configuration for the controllers on a PER ROM basis!
Just create a file that is <FULLROMNAME>.cfg (for example, I have one called "New Super Mario Bros. Wii (USA) (En,Fr,Es) (v1.02).side.iso.cfg" (Note the extension is part of this name)
You can then use any combination of keys and Wii defined buttons to redefine any of the keys (but note that you don't have to define the opposite directions on sticks and d-pads)
I personally like having my tilt on l1/l2 so my config has the following in it:
Hope this helps everyone!