I've archived my music in both ALAC and FLAC, because the Squeezebox doesn't handle ALAC files in hardware, so I use FLAC for that, and ALAC for my AirTunes. I'd prefer that iTunes ran FLAC natively, but that won't happen, but if its really that much heartburn for a guy, just download Songbird. It plays virtually every file format and has the same interface as iTunes and is compiled for all three platfroms. It is also completely free.
The one advantage of having ALACs is that they will store album art in the file, whereas you have to take extra steps to add it into FLACs. Several programs which can read FLACs require special configuration to read that album art and display while playing.
Having both file formats, a bunch of different music players, and Squeezebox/AirTunes, I find the slickest solution to be AirTunes via the iTunes interface. The files are lossless, streamable to a $99 Airport express, and if you want to get really fancy, you can use an iPod touch or iPhone or an iPad as a remote...for the whole house. For the cost of a single Squeezebox, you can literally setup 3 Airport express stereo receiving stations and use your iTunes playlist. That iTunes playlist is handy because it is already rated and organized. I could recreate the same thign on my SB, but its just extra work. And dynamic updates from anything I change on my iPod after I mow the lawn.
Right now I have Squeezebox hooked up to HT2-TLs with an AVA front end and I also have my SongTowers in my office with AVA gear as well (on AirTunes). Eventually, I'm going to go all AirTunes, which would cost me $99 bucks, so I only have to manage one set of playlists, which are usable from my computer, any of those roaming iDevices with Remote, or my iPod. I will continue to archive in both formats for insurance, storage is cheap and XLD and 8 cores make short work of converting any files. In fact, when ripping off the CD, you can set it up to make 8 formats at one time if you like. The only extra "work" is checking the box for what formats you'd like. I've tried both Max and XLD and prefer XLD myself.
I consider myself a very informed user, having messed with streaming extensively, and virtually any and all possible solutions from Microsoft and Apple (I'm a computer geek). If anyone has any questions about it, feel free to PM me. I honestly think the "work" argument is bunk, its no more work to go from FLAC to ALAC and back (or simultaneously) than it is to re-rip all your CD's from mp3 to FLAC in the first place. And it don't cost hardly more than $65 dollars to store all of it, which is dirt cheap considering people on these boards are buying 5-10K speakers and associated electronics.