NTFS overcomes many of the limitations imposed by FAT32. For instance, NTFS doesn't have a file-size limit of 4 GB, or a partition limit of 32 GB. This is very helpful if you're messing around with uncompressed video.

As for transporting files from one computer to another, there shouldn't be any problems with floppies and recordable CDs. You'll have to format the floppies with Fat32, but your NTFS machine should be able to read them.

Here's a link to an informative article on the subject:
Choosing FAT or NTFS