NTFS is a superior filesystem, wich has a better overall performance than FAT32. Basically, FAT32 is olny indicated when working wich partitions or volumes smaller than 18 Gb, or when using Windows 98.
NTFS is faster for larger partitions than FAT32, it alows encryption, file-by-file compression and it has higher tolerance to errors than FAT32.
Also, you can´t write files larger than 4 Gb in a FAT32 partition. That will be a problem in a near future, when you may have to handle DVD image files that are much larger than this.