If you're running more than one operating system on a single computer (see Dual booting in Guides), you will definitely need to format some of your volumes as FAT. Any programs or data that need to be accessed by more than one operating system on that computer should be stored on a FAT16 or possibly FAT32 volume. But keep in mind that you have no security for data on a FAT16 or FAT32 volume—any one with access to the computer can read, change, or even delete any file that is stored on a FAT16 or FAT32 partition. In many cases, this is even possible over a network. So do not store sensitive files on drives or partitions formatted with FAT file systems.
