NTFS is the best IMO.
Reasons:
NTFS constantly "tricks" the harddrive into thinking that it is full. This way, when files are added, they don't fragment up the harddrive as much as they would with something like Fat32. Also, NTFS just seems much faster and definitely more stable. Those who claim that NTFS defrags more than Fat32 have been smokin something strange and whacky
Oh yeah, for those that have systems that "slow down over time", NTFS fixes that. It doesn't happen with NTFS

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It is annoying that it is not accessible with DOS, but it can easily be fixed by using a program such as NTFSdos or the driver that Zardon dug up (see "tweaks" forum).
NTFS is also much more future proof because it can handle larger harddisks than Fat32. Also, NTFS has much more "control" over all the files. With Fat32, there are just file allocation tables and the files are just "there". (I can't get into specifics because that would require too much explaining).