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Yeah, but CD-R's can potentially be wasted <_<
Mmm, yes if you burn your music on cd-r, "wasted" as in "not playable an a specific platform". But harddrive space is cheap nowdays and still getting cheaper, so transcoding a whole collection or upgrading it when the compression standards improve is not (should not) be an issue.
Let me elaborate: There is a function "convert" in the Monkey's Audio gui, and this can be used for upgrading to a better compression (still lossless) as compression ratios evolve. Of course a whole music collection can be converted using this, very easily with drag-and-drop using a touchy-feely-clicky gui. This "convert" function can be used to convert your whole collection to WavPack for example.
The Monkey's gui needs lots of improvement, but it works perfectly as a proof of concept. Lossless music is not locked to any format, it can be transcoded any time you change your mind. (Or change your underwear)

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You can add Vorbis tags to FLAC files using metaflac, which comes with flac, but not with flac.exe itself. If you really want to do it in one command (to call from EAC, for example), it's possible to write a DOS/Win batch file or UNIX shell script that first calls flac to encode the file and then metaflac to add the tags.
Yes, that is the same way I had to do it with Monkey's, some perl to encode using MAC.exe, then tag using Tag.exe which does a very good job. For some reason I can't recollect, this worked out better than with metaflac. Hmmm, why haven't they included the Tag.exe code in MAC.exe and metaflac.exe code in flac.exe? Any developers reading this? Are there political reasons?