The following steps outline my foolproof method for setting up a triple-boot system:
Install Windows 98 on a clean hard disk. The size of the partition doesn't matter at this point, and neither does the fact that the OS will install using the FAT32 file system. This installation will be the system's C partition.
Use a disk-management utility, such as PowerQuest's PartitionMagic, to resize the partition. I recommend that you make the partition no larger than 1018MB to take advantage of a small cluster. At the same time, reformat the partition to use the FAT16 file system; otherwise the NT installation will overwrite the boot.ini file.
Insert the Windows NT 4.0 CD-ROM and use the Setup program to create a partition. Format the partition as NTFS. This configuration prevents you from seeing the NT partition while booted to Win98, but you can see the Win98 partition while you're booted to NT. Install NT on the NTFS partition, allowing sufficient space on the hard disk for the remaining Windows 2000 Professional installation.
Install Win2K Pro on the remaining disk space. Format this partition as NTFS.
I've also used this method to set up my laptop with different combinations of Windows, Microsoft Exchange Server, and Microsoft Internet Information Server (IIS) 4.0. I've never had to use an Emergency Repair Disk (ERD) because I install Win9x first, then use PartitionMagic to reformat and resize the C partition.