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.
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.
Install the NTFS–3G plugin for MacFUSE, which will allow us to not only read, but also write to NTFS drives.
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.
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. :)