A couple of years ago I did a lot of benchmarking between FAT16, FAT32 and NTFS, using a special program which allowed the filesize to be adjusted, etc.
NTFS was *much* slower when accessing lots of small files, say 1k in size. So slow in fact that it was not possible to write them to a 32x CD writer, without creating an intermediate image. This was a top-spec 10,000rpm SCSI hard disk fed off a £300 Adaptec SCSI controller, using the fastest available SCSI interface.
I now install FAT32 every time.
The main advantages of NTFS over FAT32 are
File size not limited to 4GB
Much better security; can have much finer granularity on permissions (irrelevant to most private users)
But for speed, FAT32 is probably better. I recently set up a special PC (3GHz, 1GB RAM, 100GB 10,000rpm SATA HD, top-end video card) mainly to run Pinnacle 10 for transferring HD data (over 1394) from a Sony HD HC1 cam, and it works better when writing the stuff to a FAT32 partition than an NTFS one.
BTW I am not happy about that other thread getting locked, especially as nobody actually answered my question.