iTunes for both Mac and Windows can (with an additional QuickTime component) play FLAC and OGG but apparently not FLAC in the standard file format (only in the Xiph format). See
http://www.xiph.org/quicktime/download.html
This workaround (Mac only)
http://barelyfocused.net/blog/2006/10/12/native-flac-in-itunesquicktime/ helps get round some of those problems. Basically it is an alternative FLAC file parser and still uses the Xiph FLAC decoder. Even this does not provide perfect tag support but should let iTunes play FLAC files in .flac format on a Mac.
Personally I would suggest you go the Apple Lossless route. I have all my music in Apple Lossless and can and do share it successfully between :-
iTunes (Mac and Windows versions on a dual boot Bootcamp setup)
WMP 10
Media Center 2005
Roku SoundBridge
SlimDevices SlimServer
SlimDevices SoftSqueeze
it will also work with :-
iPod
AppleTV
Sonos Zone Player
and even (via MCE 2005 & WMP 10) an XBox 360 Media Extender!
It is also possible to use Apple Lossless in Foobar 2000 and WinAmp (as well as WMP).