win 2000/NT default use NTFS, win XP deafult use FAT32..any other lower version use win16 format...
Difference its on how it arrange the file structure... transparent to user though
Win XP are able to access to NTFS and FAT32 file structure....
Basically when u install the OS u will be prompted which format u wan to format at, pior to the installation itself... if u r using 2000/XP u can still use the "administrative tool" under control panel to format/del/add those unused partiitions....
Other than that u can also try partition manager at softseek.com just get the trail version its ok anyway u won't be using it after that.
Hope that helps.