I too have QT on many of my systems (the ones where I need to use iTunes for my phones, and my Macs of course), and I agree... It isn't too bad if you take those two steps. Just annoying that you have to take them.
Interesting...
I currently have MC create LAME VBR -V5 stacks for syncing over to my iPhones to save space. That works fine, but sometimes the quality is noticeably bad. Perhaps more importantly, there is the fact that MC doesn't handle having two different versions of a file in the same container format very well if you have it stack the files "in place" (they just end up named "-1.mp3" which is annoying and confusing if you need to manage the files manually ever). It is fine, of course, when I'm stacking from a FLAC source, but many of my library files are LAME -V0...
If I switch my conversion encoder for the handheld to AAC, that would solve the problem in most cases and get me a bit better quality to boot.
I'd be very interested to see your recommendations, Alex, when you get them done. I actually have QT installed on the server machine already (and I keep it updated), so using QT would be simple.