Is your partitions are in the same Hard Disk?
.unicorn made an excellent post in this thread regarding it:
http://www.betaone.net/forums/index....T&f=43&t=18744 based on his personal experience.
It might help you to get a decision.
Personally I prefer to have all partitions with one file system, as long as I use only Windows 2000/XP
Please be aware of the fact that when you convert a FAT drive to NTFS, the cluster size becomes 512k. If you like it then it is alright. But if you don't I think you will better do it by Partition Magic.