i would recommend NTFS, from what I've heard it's better for harddrives that are 30+ gigs. Also it uses much better file incription hence the better security than fat.
NTFS is much better. FAT32 is plagued by performance degradation with larger hard drives and is highly inefficient with large partitions. With a 40 GB hard drive, FAT32 clusters are 32 KB and with NTFS it is 4 KB. Then there is stuff like security, etc. that is missing in FAT32.
Honestly, the only reason I would tell you to use FAT32 is if you have a dual-boot configuration with the old Windows 9x/ME family, which doesn't recognize NTFS formatted drives.
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