Itīs not easy to say which filesystem thatīs the best. NTFS is better if you are looking for higher security, FAT32 is faster though.
Iīm running win2k with NTFS. The conversion is easy as the win2k setup does it for you (If you want to).
When I installed win2k I did it on a formated, empty harddisc so it was done really fast and easy. A friend of mine did it on a not-empty disc and said that it took really long time (around 1 hour) to convert.
I think NTFS works really fine for me.
/bucky