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I prefer Fat32, but that's just because you can actually access it if the OS corrupts. (really a pain when you can't back up your information because of a registry file error.)
Just my opinion tho, I use Fat32 for C drive(about 5Gig), NTFS for the other drives. This way I can also ghost an image of the contents, not the complete structure(1Mb file would take an image the size of the complete drive.)
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