In some cases, no third application programs are required. I have a triple boot WinXP_PRO + Win98SE + DOS 7.10a, and I don't use any third application programs.
I created and formated a primary partition, leaving unpartitioned space and installed Win98 on that. Then, I installed WinXP using the unpartitioned space (created a NTFS partition with the WinXP installation itself, on the unpartitioned space), and WinXP automatically detected my other OS and gave me a boot option.
About Win98SE+Dos7.10, that's just a little CONFIG.SYS / AUTOEXEC.BAT / MSDOS.SYS trick.
If you're using Windows NT or a later version of Windows that uses the NT OS loader, you can use that to boot everything (except installastions of OS/2 Warp installed on HPFS partitions--for some reason, the NT boot loader isn't compatible with that.) I use the NT boot loader to multiboot MS-DOS 6.22, MS-DOS 7.1, Windows NT 4.0, BeOS, Solaris, and Linux. Note that this is a violation of the EULA.
If you've got Linux, you could boot everything using GRUB. (You *could* use LILO, but LILO relies on INT13 BIOS routines and is thus subject to BIOS limitations.) GRUB is free and works quite well.
Another excellent free boot loader is XOSL (the eXtended Operating System Loader). It might be a little cumbersome to set up, but it's well documented and works great.
If you want to spend some money, V Systems' Boot Commander works quite well and has some nice little bells and whistles.
I just take advantage of my BIOS ability to boot from more than one drive. For stuff I seldom boot, like a backup copy of Windows, I have a second disk drive, and can change the CMOS BIOS settings to boot from the second (slave) disk drive. A bit tricky to set up (normally have to make the drive a master, FDISK,format and install, move to slave and put master back in).
Having a stripped down backup copy of Windows is great for running Defrag on the first drive. This way you can defrag even the swap file and run scandisk on the first drive when it has boot problems. Also allows you to do a backup of the other drive.
You mentioned using the NT loader for also booting into Linux. I couldn't do that... After installing Win98 and WinXP to different partitions, I still had some reserved space for Linux (Red Hat). I booted with the installation CD, and installed Linux (created new partitions for that). It asked if I wanted to use that GRUB, LILO or keep using the current boot handler. I said it should keep the current boot handler.
I'm on WinXP_PRO. On "disk management", it sees 3 new partitions (other than C and D, which are for Win98 and WinXP). The information for each one of these is the same:
What should I do? Maybe I've done something wrong on the Linux installation. I had some options like "boot mount" and file system (which I reckon was "(something)3")... I don't know anything about UNIX systems, I'm willing to learn.
If you want to use the XP boot maneger(i don't know anything about XP) then don't install any linux boot loaders at all I use the boot disk option for this myself which works great but a bit slow so I created a multi boot CD using CD-Recordable Package version 1.2 (c) 2001 Bart Lagerweij http://www.nu2.nu/contact/bart