using the disk cleanup and defrag utilities a short while ago i noticed my c drive was ntfs file system and my usb external drive was fat 32 file system.i,v had no problems but did wonder about the difference.any reassurance would be welcome.
personally, if a drive is under 40 meg, i choose fat32 because ive noticed its a lot faster, especially with games. The drawback is, it wont support files over 4gig. I use ntfs on all my 200gig drives tho
I too have two hard drives I would reccomend having the C: drive as NTFS as it is easier to recover after a crash and have any other drives as FAT 32 as it is faster and is not used as much as the c: drive theres less chance of it crashing. I hope this helps.