Hi there bierfeldt,
From a technical perspective there is really nothing to choose between FLAC and ALAC. Both achieve a similar end by very similar means and there are absolutely no quality pros or cons that I am aware of. IIRC ALAC has some specific features to support Airplay streaming, but as far as substantive differences go that's about it.
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Apple placed ALAC in the public domain under the Apache license a couple years ago (although not before a bunch of folks had spent a lot fo time and effort reverse engineering it), so now presumably all 3rd party devices are using encoders and decoders are based on the Apple source rather than the Hammerton/Brocious code (which still had some bugs in the hi rez code paths when I tuned out a few years ago).
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iTunes (vanilla) still doesn't support FLAC and I'm guessing that WMP (still) doesn't support ALAC. Otherwise I think most all replay environments support both and so it is probably moot. Converting between the two is also pretty straightforward so this isn't the $64k question it once was.
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Good luck!