So as per the suggestions of a number of people, I went ahead and started ripping my entire CD collection as APE rather than MP3 (so far I'm about 1/4 of the way through). I'm now building a great library of my original CDs without any sort of compression artifacts.
This is great for my RAID array on my home PC, but now I've realized I want to transfer some songs to formats where space is at a bit more of a premium, such as CD-Rs for my MP3 car stereo, and to my PDA. In the case of the PDA, I have to re encode the files as MP3 every time I transfer them over, which is a waste of time. But if I want to create a CD-R with MP3s on it, I've got a lot of hoops to jump through. I am now forced to re encode the APEs to a new directory, locate that directory, and then burn the files from there.
So here's my suggestion - for audio files there should be at least two separate files referenced in the library - a Lossy version and a Lossless version. There could then be a function to automatically generate a lossy version of any file (choose your flavor, MP3 WMA, Ogg, etc), or select a pre-encoded file, and have it be referenced as part of the same library entry. When burning files to disc or transfering to a player, you could then have the option of which version of the file you would like to transfer over. While I've simplified my suggestion here, it hopefully would be possible to not just have 2 versions of the file, but many more, so that you could have a 32 kbps WMA file, a 128 kbps MP3, a 192 kbps Ogg and the original APE (or however you want to break it up to best suit your needs) for the same song, so that the you always have the correct format on hand for whatever situation / device you need it for. When properties are changed, MC would update the tags automatically, so everything stays in sync.
Of course, this is perhaps too ambitious. I've explored having both MP3 and APE versions of the song in the library and then filtering, but it is a management nightmare. If I have a playlist that I want to transfer as MP3, I have no easy way of knowing which files I've converted, short of converting my entire collection to MP3 - it'd be nice if files could be converted as necesary. Also, any changes made to the APE file (ratings, genre etc) will have to also be made separately to the MP3 file. If anyone has any great ideas about how to better keep this sort of system in sync, I'd love to hear it, since so far it hasn't been working out too well for me.
As an interim measure, it'd be really nice if there were a one-step way to select files from a playlist and have the option to automatically re-encode them to MP3 before burning to disc, but ideally there should be an easy way to store these mp3 files once they've been encoded so that they're ready for the next time I need an MP3 version, thus my suggestion above.
Thoughts?
--Tim