I was trying to figure out how to hide my Boot Camp NTFS drive icon from my desktop, and after some searching I discovered a relatively simple 4-step process. If your Boot Camp drive is FAT32, you can skip the first 2 steps, and begin with step 3.
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Install MacFUSE. This is a Google project that allows you to mount other file systems on your desktop, including even things like SSH and FTP.
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Install the NTFS–3G plugin for MacFUSE, which will allow us to not only read, but also write to NTFS drives.
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Install the Mac OS X Developer Tools. They should be an optional install on the Mac OS X install disc, or I believe you can download them manually.
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According to Garbage In, Garbage Out, simply copy-paste this line into your Terminal, and press Enter:
/Developer/Tools/SetFile -a V /Volumes/Untitled; killall Finder;
Your Boot Camp drive icon should be hidden from your desktop, but may still show up in things like open/save dialogs. :)