Apple lossless is the way to go in iTunes.
I like to be able to update iTunes whenever a new version arrives and depend on easy syncing across computers (home sharing and streaming) as well as across devices so I try not to add plug ins or non-supported formats unless the need is great.
If you are worried about the proprietary nature of Apple Lossless instead of FLAC (the best free lossless alternative), it is very simple to batch re-encode the entire library to AAC / MP3 or AIFF/WAV or burn to a CD at full resolution.
The benefit of stock Apple Lossless format is about 50% compression rate with no loss of data or sound quality.
I would guess most people that don't use an external DAC and premium headphones ($400 to $1500) with audiophile amplifiers will rarely need AAC bitrates more than 240kbps for most recordings. Going higher is generally a waste of space for little to no discernible impact on listening enjoyment.
Basically, it's only worth encoding higher if the recording is precious and archival in nature or you really do hear a difference for that one piece that makes it worth re-encoding at a lossless level.
You can always start with Apple Lossless and convert later to FLAC/AIFF or downsample if you feel constrained by Apple's software.