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It depends on whether or not you want a file system that has native compatibility with many OS'. FAT32 is a good one for that but it lacks in other areas. NTFS is good because it supports journaling- helps prevent errors to your hard drive in the case of power failure- while FAT32 does not.
Unless you dual boot linux and windows, or plan on putting that hard drive in a mac machine, you shouldn't have to worry.
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