The most obvious way to use mp3 files in mods would be to hack the part of the exe code where the org data is interpreted and outputted as sound and rewrite it so that it interprets mp3 data instead of org data, but that would be ridiculously difficult.
What andwhy is suggesting is that for each org voice, there is some raw sound data in the cave story exe somewhere for what that voice sounds like. If you could replace that data with the audio data from your mp3, and then use resource hacker to put in an org file containing a single note held for the duration of your mp3 file at whatever pitch the pitch of the audio data in the exe represents (probably either middle C or A-440), then the file would still technically be in org format, but it would play the audio sample that you want rather than the standard org audio samples. Also, andwhy, my guess is that the exe does not contain an audio sample for every single note possible in organya (that would use a lot of memory), they probably just have one audio sample for each voice at a certain pitch (like I said before, probably C or A). In other words, you probably shouldn't be looking for a note that is never used in cave story, you should look for a voice that is never used.
What Lace is suggesting is that you change the file extensions on your org files to mp3, and hack the exe so it accepts mp3 files rather than org files. This would probably work, except that it wouldn't accomplish the goal of using mp3 data in cave story. The sounds produced would be organya sounds. The org data would still be org data, and would be interpreted as such, it would just be named differently.