While the preferred file system for releases of Windows from Win 2000 and later is NTFS, in the interest of backward compatibility there is still support for FAT32 systems. While you can set up those drives in this way, it's not the easiest thing in the world to do, in addition to the fact that there are some severe limitations imposed by Windows itself. So if you've got a big drive and you need it to be set up for FAT32, you could easily be out of luck.
Fat32Formatter is a tool that can help you work around those limitations. It's got a sparse, easy-to-comprehend GUI, which puts it worlds ahead of any kind of command line tool. Select your physical drive, pick a partition to initialize or remove, and you're off to the races. There's no installer for this tool—you just unzip the tool into the directory you want it to live in—so there's not a lot of extra junk to clog your system up.
You can grab a copy of Fat32Formatter for free. It requires Win2k or later.