I've created a free small app called iCleanup to deal with volumes that are being used with Mac OS X as well as Windows -- USB memory keys, for example. The problem with these volumes is that your Mac litters them with hidden files. Windows users can see these files, but they have no use for them.
iCleanup deletes .DS_Store, .Trashes and ._ files from a selected volume and optionally unmounts is. I hope some people will find it useful.
[robg adds: Though we have a few hints on removing .DS_Store files from Unix machines and CDs, we don't have a hint on removing them from Windows machines. I downloaded the app and looked at the AppleScript inside the iCleanup package. It looks relatively benign, but still, it's deleting files, so having a recent backup before running it is a good idea.]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20040726164957299