I don't use NTFS except for a dedicated virtual memory partition. The reason being it cannot be remotely manipulated. Windows 98 SE and ME cannot read the NTFS file system...... PERIOD. Only Windows 2000 and XP can.
And, once the Windows interface has loaded, you can't delete certain files, it is impossible, Windows/your PC will 100% prevent you, and I'm not sure anyone has been able to hack around this.
So if you want to delete "Index.dat", which secretly logs all online actitivty (it can be found in your Cookies folder in 98 SE), it is not possible to do it without reformatting. The same thing if you wanted to delete a file critical to running Windows (like your IO.SYS). If you try to delete it you'll get an error message saying "Cannot delete, move, or rename file, it is currently in use, active in memory, or required for running Windows" something of that nature
So, the only way to remove those files is to do a complete a complete reformat, which totally sucks and is way time consuming. That is, of course, for NTFS
The only other option is if you have another harddrive, and boot of that. Then you can delete the files on the other drive - but of course, you'd need Windows 2000 or XP installed on the drive you booted off, which means you need 2 harddrives, both with Windows 2000 or XP installed - which really doesn't make sense to me. If I have an additional harddrive, I'd use it for backup and have a different OS in it.
However, with FAT32 there is another option. That being you can delete them from pure MS DOS mode or a Windows 98 startup disk.
So anytime I want to wipe my SWAP file, I will just shutdown 98 SE with "restart in MS-DOS mode", delete win386.swp, then as soon as I type exit and go back to Windows, it will be replaced. Much easier than reformatting or messing around with other drives, boot settings, and master/slave config (and other time consuming crap).
The only real advantages I see in NTFS are, it doesn't require defragmenting as often, and it is more "stable". Other than that, I have no use for it.
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