This would be useful for those of us with old and obscure controllers that are only partially supported (ie, you can map some buttons but not all). With the built-in controller support disabled, we could then use a third-party app like xpadder to map everything according to our needs.

I know that the "easy" solution is to just use a supported controller, but some of us like to make things difficult.

Thanks for the suggestion but I just figured out the easy way after finding the save folder.

HOW TO DISABLE NATIVE CONTROLLER SUPPORT

1. With Doom 64 closed, open this file in a text editor:
C:\Users\[Account Name]\Saved Games\Nightdive Studios\DOOM 64\kexengine.cfg

2. Find this line in the above file:
seta in_nojoy "0"

3. Change it to:
seta in_nojoy "1"

4. Save the file. You're done.

This should clear the way to manually map all buttons in your joypad mapper of choice.

EDIT: Another way is to just delete some or all of the "bind joy_" lines in the above file. This might be preferable if your analog sticks are already working and you don't want to have to map them to mouse emulation.