Depends on the version of DOS, but the earlier versions only did FAT16. Later ones did FAT32.
Win9x = FAT32. WinME is, at least by default, FAT32. I don't remember if it can do NTFS.
Win2k/WinXP/Win2k3 are all NTFS.
Windows XP will let you format the drive before installing, just delete any existing partitions during the "DOS-looking" setup, then recreate them, and it will ask you for either FAT32 or NTFS (you want NTFS). It'll then format it for you.
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