Opinions will and do vary.  This thread concerns audio files, but scan it anyway. Perhaps you'll glean something from it to help you decide.  Personally, I think it's a wash - but I don't move large files back and forth often:

http://forum.nuendo.com/forum/Forum1/HTML/008142.html

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@stewartshine wrote:

Hi,

I've just bought a new Dimension 8300 with a 120Gb IDE HDD.

This is formatted as NTFS.

I have installed a 2nd 80Gb IDE HDD with loads of data from my old system.

This is formatted as FAT32.

Transfer between the 2 disks seems slow.

If I reformat my old 80Gb as NTFS, will this have a significant impact on data transfer between the 2 disks ?

TIA for any help and advise.

Format does NOT matter, IMHO.  I run several systems with both formats.  However, I would check the following things:

1) Is the old drive on the same channel as secondary, and set to cable select?

2) Is the old drive, in BIOS, showing the proper transfer speed?

3) If yes to #2, is it ATA-100?  or ATA-133?  If it's really old (ATA-66 or slower), that could be an issue.