If you mount unix servers via samba you probably end up with .DS_Store files all over the place. A way I found to keep those from showing up is to 'veto' these files in the Samba config. In the [global] section of smb.conf of the server I am mounting I added:
veto files = /.DS_Store/[Editor's note: I haven't tested this one yet...]
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http://hints.macworld.com/article.php?story=2003011306415910