Thats what Pakkiso does.For CDDA-music, which is what we are talking about here, only wav AFAIK. Sometimes cue-sheets list all tracks as ".bin". So if you converted the APE-files to wav, you might want to take a look at the cue-file with an editor afterwards and if necessary edit the names in it from ".bin" to ".wav" except for the first (non-audio-)track. Renaming the wav-files to ".bin" might also work.