NFTS is by its nature, going to be slower than FAT32 because it has all the security to deal with. BUt still, the difference sin speed is not worth the pety(yes, pety) improvement.
FAT16 is worthless now...it addresses the data with only a 16-bit depth, allowing for only 2GB max...don't quote me on that last one.
NFTS is the king, for windows anyways....the LINUX file systems are great too...