The opinions (and analysis) presented here do not necessarily reflect those of the DAISY Consortium.
APE is as a possible solution for consideration. Information can be found at: monkeysaudio.com.
I recommend FLAC over APE. And WavPack looks really good too.
It would be a great boon to offer fully integrated FLAC/WavPack support in DAISY production tools... it would give instant archival storage savings of greater than 50%.
It would be nice if a DAISY production tool had an option such as "Pack that project for transfer" using one of these open source codecs.
I would recommend FLAC over APE, because FLAC has excellent error recovery, while APE does not. I did some unscientific tests on FLAC a while ago, inserting random data into a compressed audio file, changing data at random, and deleting data. The FLAC decoder reported all errors, and continued decoding after them, substituting silence for the bad data. There is a good summary at: hydrogenaudio. I haven't tried WavPack, but it and FLAC come out on top.
I have used APE for quite a while and haven't had occasion to find fault with it, although testing was limited to random and periodic decompression and verification. It has a good command line executable, which allowed me to make a simple batch conversion interface running in the background at off-peak processor times (at night), which I think is important. I did initially test the "stop processing on encountering error" feature, which does work but indeed doesn't provide a fix. I use it for archiving only, so the fact that both the compression and decompression are slow doesn't matter, but this may impact your intended use. I haven't used FLAC so can't compare.
I've done my own unscientific tests with FLAC 1.1, using the default options. I found I got slightly worse than 50% compression on 16-bit 22.05 kHz files (analogue tape conversion) and slightly better than 50% on 16-bit 44.1 kHz files (original digital recordings), both at a reasonable speed. Your mileage may vary, of course, depending on how much background noise there is. Hans Heijden's comparison page is at: hvdh. This link (which is somewhat out-of-date) has some excellent graphs, which show that FLAC is somewhat lagging behind most other modern encoders in terms of compression rate and encoding speed (at least for his music collection). Where it shines in a technical sense is in decoding speed; it outstrips all the other codecs by a wide margin.
We have used FLAC for one year for production backup. We don't have any problems with decompressing. The compression average value for almost 1100 DAISY books is 53%. The compression performance is 5.78 MByte per seconds on a Linux SuSE Box with 2 XEON Intel(R) Pentium(R) III CPU 1400MHz.