In today's (unusually late) DOOM 3 newsbit, a post on
PlanetDOOM confirms from
Activision that DOOM 3 will not run under Windows 98 or Win98SE, but that
Windows XP or Windows 2000 will be required.
Well for one, NTFS has large file support (ie: DVD image files). As a home user you probably aren't going to notice a whole lot of difference between the two.