I just thought I'd put in my 2 cents:
After viewing a number of posts about NTFS vs. FAT32, I thought I'd give NTFS a try. To give both filesystems their fair trial, they both were fresh installs with exactly the same software installed. Well, I found it was more trouble than it was worth. Reasons:
1: Multi OS boot: I have Win98, XP, and Linux on one drive. The other 2 OS's don't let me access the NTFS partition without a fair bit of tweaking or third party software. FAT32 mounts all by itself in Linux (Mandrake 8.1), and 98 sees XP under FAT32, so grabbing files is a breeze.
2: Speed: It wasn't VERY noticeable, but I did perceive a slight increase in application speed with FAT32. Maybe its because I am biased towards FAT32, but thats my opinion.
3: Security: My PC is on a 2 PC peer-to-peer network with no Internet sharing (both PCs use dial-up 56k AOL independently), so security is not a concern. I am not arguing NTFS is more secure, I just don't need it.
4: Reliability: I guess I would need to run both filesystems for an extended period of time, but I still have a 2.5 gig drive (WD) formatted as FAT32 that still works great.
5: Filesystem efficiency: I know NTFS wastes less space due to more optimized cluster size, but I have 2 fairly large drives, so space isn't a real concern of mine either.
So, to sum up: If you need security or a more efficient filesystem, go ahead with NTFS, otherwise FAT32 works "well enough" for general use. Again, these are my opinions.