Stick To NTFS On Windows
It’s hard to maintain a consistent benchmark suite that is applicable across all platforms (Windows, Mac, Linux, and so on). We've begun to touch Windows and Mac in our drive reviews. However, for this piece, we stuck to Windows and used FAT32, NTFS and exFAT, representing a vast majority of desktop users. Moreover, exFAT is poised to become one of the few file systems (other than FAT32) that is supported on a variety of operating systems due to its inclusion in the specifications for SDXC cards and upcoming digital devices.
If you're using a Windows-based system, stick with NTFS. The default Windows file system consistently delivers the best performance on both SSD architectures we used for these tests: Samsung’s 830 series and the SandForce SF-2281 controller, represented by Zalman’s F1 drive. NTFS also has the advantage of being readable on various non-Windows operating systems, making it partially cross-OS-compatible.
While FAT32 has the advantage of wider platform compatibility, we don't recommend it for anything other than USB flash drives or the case of operating system environments that include Windows versions prior to Windows XP SP2 (and in that case, there are other, more serious issues to consider). Its lack of file access permissions, free space bitmap, file journaling, and basic performance make it pale in comparison to modern file systems such as NTFS and exFAT.
Between exFAT and NTFS, it's almost a draw. NTFS's robust file permissions control puts it ahead of exFAT for an internal storage device, but exFAT's tolerance of hot-plugging make it a definite choice for USB-connected storage. As we mentioned earlier, FAT32- and exFAT-formatted drives cannot be used for modern operating system disks. But for users who like to have fast access to data, or who prefer to install programs on a different drive than the OS, these arguments begin to make more sense. In general, though, we're going to side with the experts (and Windows) on this one: stick with NTFS if it's internal, and use exFAT only for external storage.