NTFS
Default files system in windows xp, 2k and NT.
Support for Drives over 40GB to 2TB Files over GB.
Allows extended file names, foreign characters.
Has a severely crippled maintenance system in chkdsk.
Chkdsk is notoriously slow.
Increased security with file encryption
Faster on drives less than 40GB.
Smaller file clusters, 4kb.
Compression to reduce disk space.
User permissions for files and folder.
File copies are “undone” if interrupted cluster is cleaned.
Small files are kept in Master file Table at beginning of the drive.
FAT16/32
Fat 16 not compatible with xp,Fat is more compatible with other operating system (windows 95,etc)
Support for Drive over 32MB to 2TB
FAT 16 has 8.3 character limitation
Has better more and interactive recovery utilities
Scandisk is very quickly
Just a space for the OS to read files
Faster on drives less than 10GB
Fat 16 cluster size is 32kb
No compressionSame as NTFS
Cluster chains containing data from interrupted copies are marked as damaged
Master File table are separate from files.
Source.