If you are using multiple OSs on the same computer (Windows XP and Windows 9x) and you want the two OSs to read the drive, FAT32 is the only way to go.
But, if you are planning on only using Windows XP, NTFS is the way to go.
There are several reasons why NTFS is the way to go.
One of the highlights of NTFS is the protection that it provides for files.
To ensure reliability of NTFS, three major areas were addressed: recoverability, removal of fatal single sector failures, and hot fixing.

NTFS is a recoverable file system because it keeps track of transactions against the file system. When a CHKDSK is performed on FAT or HPFS, the consistency of pointers within the directory, allocation, and file tables is being checked. Under NTFS, a log of transactions against these components is maintained so that CHKDSK need only roll back transactions to the last commit point in order to recover consistency within the file system.

Under FAT or HPFS, if a sector that is the location of one of the file system's special objects fails, then a single sector failure will occur. NTFS avoids this in two ways: first, by not using special objects on the disk and tracking and protecting all objects that are on the disk. Secondly, under NTFS, multiple copies (the number depends on the volume size) of the Master File Table are kept.

In NTFS file systems the security is high compare to fat 32.

In NTFS the max drive size is 2 TB. In fat 32 the max drive size is 32 GB

FAT 32 does not provide system file security, wherein ntfs provide it.

IN fat32 the compression level is very low campare to ntfs moreover NTFS support large network protocols.