You can use Fighter Factory to open your [mugen]\data\common.snd file and replace the sound entries 7-0/7-1/7-2 with your own fall sound WAV files. This way affects globally.
Also you can add your own fall sound WAV files to your own MUGEN character then duplicate the falling state and overwrite its Statedef 5100 & 5110 with the PlaySnd of the different values. This way affects individually.
For example, include your own common1.cns file, or just overwrite the particular states in your MUGEN code:
; Downed get-hit (hit ground from fall)
[Statedef 5100]
.......................
[State 5100, 10]
type = PlaySnd
trigger1 = Time = 1
value = F7, (sysvar(1) > Const720p(20)) + (sysvar(1) > Const720p(56)) ;<== replace this value with your choice, i.e. value = 5100,0
; Downed get-hit (lying down)
[Statedef 5110]
.......................
[State 5110, 6]
type = PlaySnd
trigger1 = Time = 0
trigger1 = !SysVar(0)
value = F7, (sysvar(1) > Const720p(20)) + (sysvar(1) > Const720p(56)) ;<== replace this value with your choice, i.e. value = 5110,0