By the way, w/ respect to your comment about having to edit your sound files to make them useful sound cues: This is sort of the tedium of sound design in games. Pretty much all sound designers have to deal with this. Even if you had a cool tool to do the sound atlas, you’ll probably still have to go through the tedium of authoring the cue/loop points (though, I could implement a threshold-detector and give you audio “slices” like Reason’s Dr. Rex player, which would be pretty cool).
So, in the past, on other games I worked on, I solved this tedium (or at least reduced it) by using sox, a really nifty swiss-army-knife audio command line tool, and generated my asset slices from single given source files (and did the usual normalization, etc, while I was at it).
And here’s a tutorial on how to use it to split up an audio file based on silence thresholds:
Then you would use whatever language you want and call the command-line tool sox.exe with the proper files/paths based on whatever conditions you want.
Googling, I also found this which you might want to check out: Easily Split Audio Files with WavePad Free Audio Splitter
Also, various DAW’s do batch processing/export, which might also be a solution for you: