When I knew I was going the route of using an iPod, I researched the "best" way to store files and I quickly learned that there are many opinions on this. This led me to do a couple comparisons myself comparing AppleLossless, WAV and AIFF. In the end, I could hear no difference between them.
Having done this, I am comfortable in my choice of using Apple Lossless and saving space. If others feel there is a difference, it does not sway me.
FWIW, here are a few quotes...
"As expected, the iTransort sounded like the DAC to which it is connected. I store my music on my iPod using Apple Lossless, which provides perfect bit-for-bit accuracy to the original with about a 40% reduction in storage requirements compared wit uncompressed WAV files. In listening comparisons between the iTransport and the CDs from which the music was ripped, I thought the iTransport had a slight advantage" -- Robert Harley, TAS Issue 186
"...You're actually given 3 options in iTunes---Apple Lossless, WAV and AIFF---which preserve digital files losslessly. Any of these deliver CD-quality music." -- Steven Stone, TAS Issue 183