I tried XiphQT earlier with iTunes and liked the fact that it let me play OGG files.
As for FLAC, I just used foobar2k to make a CD Image out of the FLAC files, made DAEMON Tools mount the .cue as a CD, then I used EAC and
iTunesEncode.exe to make Apple Lossless files out of them.
If you already have EAC installed and know your way around it, here are the command line settings you'll need for iTunesEncode.exe if you want your Apple Lossless files to be tagged properly. Just leave iTunes open while ripping with EAC and iTunesEncode will parse all the tags from EAC over to iTunes and it'll take care of tagging them.
-e "Lossless Encoder" -a "%a" -l "%g" -t "%t" -g "%m" -y %y -n %n/%x -c "%e" -i %s -o %d -d