The indexing you are referring to Alan is only for faster file searching and has no bearing on audio performance. In fact, any tweaking guide you can find will recommend to turn it off.
NTFS is actually slightly slower than FAT32.
But NTFS performs better on large partitions, has better stability and security.
One thing to watch out for though, any Windows 9x version cant read NTFS at all. You\'ll need either; NT, 2000 or XP to read an NTFS drive. (In fact they read both file formats)
There is a story about Chance Thomas getting caught out at a studio, he brought his NTFS drives in and the studio had Windows ME. Apparently the studio sorted it out but it is something to keep in mind, NTFS wont be compatible everywhere.
Having said that though, all Windows 9X version are in decline and will no longer be supported. I styick with NTFS for greater drive security and better performance on large (+20 gig) partitions.