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I'm pondering using a dual strategy of FLAC or Apple Lossless as an archive format and then down-converting to MP3 for the car, the iPod, and so forth.

If you are going to do it then you might as well use FLAC in the first place since it'll be easier to transcode to other things due to the proprietory nature of Apple Lossless. There is an opensource decoder for Apple Lossless but it doesn't support some features yet.