I was up too late last night reading about lossless codecs at Hydrogenaudio. The outcome of that research is I'll stop simultaneously encoding in two lossless formats, ALAC and FLAC. My primary music consumption is iTunes playback through a good receiver with speakers and a iPod Nano. ALAC (Apple Lossless Audio Codec) becomes my primary format. I thought about FLAC as a hedge, but it appears there are tools just mature enough to allow transcoding from ALAC to FLAC if I ever need it. They both are lossless formats, thankfully.
So I'll continue to use Yahoo Music Jukebox for music and radio recommendations and to checkout new music I might want to purchase, and iTunes will be my primary jukebox and playback tool.