I came across a nifty little python script called, "iPod shuffle Database Builder", or rebuild_db.py, which allows you to take full control of your iPod Shuffle without needing iTunes. It allows you to manage the audio on your Shuffle by using the Finder.
I recently bought an iPod Shuffle to compliment my 20 GB iPod. The Shuffle appealed to me because of its small size and built-in usb connector. I planned on just keeping it in my pocket at all times and being able to copy talk radio shows to it from my computer at home, at work, or anywhere without the hassle of having a cable with me. I was rather disappointed to find out that in Apple's feeble attempt to stop music piracy they also make life a real pain for everyone, especially those with more than one computer.
Say you download an audio file of a radio show and want to quickly put it on your MP3 player. With other players, you just drag and drop it. With the iPod Shuffle, you have to first import the file into the iTunes Library, then drag it to your Shuffle. While annoying, that is not the bad part. The real annoyance appears when you plug your Shuffle into another computer. If the iTunes application is open on the machine (any machine!), the Shuffle will automatically get updated with no warning. And by updated, I mean any audio file that does not appear in the iTunes library of that machine will get deleted.
With my normal iPod, I at least get a warning window asking if it should sync with this new computer. With the Shuffle, there is no way to disable this. All you can do is uncheck a box that says "Open iTunes when this iPod is attached". But if iTunes is already open, it still will delete audio files that don't appear on the machine with no warning. This seems like a serious bug since the Shuffle can also be used as a normal flash drive for transferring files to different machines.
An alternative is to ignore iTunes altogether and use the rebuild_db python script.
To manage your songs manually:
cd /Volumes/NAMEOFSHUFFLE
./rebuild_db.py
The script will search for audio files in all folders on the iPod Shuffle, then update the Shuffle's music database files.Mac OS X Hints
http://hints.macworld.com/article.php?story=2005040610284411