My tool is sort of overkill if you just want to rip the samples into WAV, but why not. You can either use Viena sound font (a free GNU clone of Vienna Sound Font) to rip the WAVs from the sound font that is outputed by GBAMusRiper. Alternatively, if doing it for just a couple of samples, you could use it to see the starting address of the sample(s) you are interested in, and then extract that data with a HEX editor. The sample's length and loop point (if existent) are specified in the 16-bytes header. Since the data is 8-bit signed you probably want to use audacity, use its "import RAW" functionality and save as a proper WAV.
PS : As for Mother 3, I have no idea which of us is wrong on whether the game uses or do not use the sappy engine. In the last version, I switched from my own crappy detector that would cause lot of false positives and false negatives to the detector written by someone else and that looked to be a lot more accurate. Be sure to use the last version.