there are a few reasons to keep FAT32, they all involve the fact that a Win9x computer can't read an NTFS partition. If you have network that needs to be accessed by a 9x machine, then you need to keep FAT32.
I have a WinME machine that needs access to files on a WinXP machine. What I do is create a Fat 32 partition for all the files that need to be shared, and keep XP and everything else on an NTFS partition.
There are also partitions for Linux, but they don't show in XP