The clipping is due in large part to the ultra high compression employed in most of today's rock/pop/hip hop recordings (both new and remastered "old" albums). Though the iPod seems to be a little bit more prone to clipping, I have many CDs that clip on portable CD players.
I've found that reducing the gain using a gain normalizer like MP3Gain (download
HERE) has helped the situation greatly. There is also a Mac version of the software called MacMP3Gain that can be found
HERE. As I am a Windows user, I cannot vouch for the Mac version.
I have found that reducing the album gain to 92 or 93dB gets rid of much of the clipping. However, some albums are just too far gone (check out Metallica's "Death Magnetic" for the absolute worst example of the dangers of over-compression).
Just re-read your posts (you mention iTunes downloads)- I do not know of AAC gain normalizers for the Mac (though I'm sure there is something out there); there is AACGain for Windows
HERE.