If you only want to do a 1:1 copy, Nero or any other copy program works. You only need to use an ISO editor to inject files and still keep the existing boot sector so the cd still boots.
There are other ways, but I usually just make an ISO of my XP/2000 CD, then add or remove files (such as when I slipstream with a SP or add utilities), then burn the new ISO image that is still bootable.