Try this batch:
---------------------------------------
[/i]@echo off
if "%windir%" == "C:\WINDOWS" goto 98
if "%windir%" == "D:\WINNT" goto NT
:NT
ECHO Switching OS To Win98
DEL C:\BOOT.INI
ECHO [boot loader] > C:\BOOT.INI
ECHO timeout=8 >> C:\BOOT.INI
ECHO default=C:\ >> C:\BOOT.INI
ECHO [operating systems] >> C:\BOOT.INI
ECHO C:\="Windows 98 Second Edition" >> C:\BOOT.INI
ECHO multi(0)disk(0)rdisk(0)partition(2)\WINNT="Windows 2000 Pro" /fastdetect >> C:\BOOT.INI
GOTO REBOOT
:98
ECHO Switching OS To Win2000
DEL C:\BOOT.INI
ECHO [boot loader] > C:\BOOT.INI
ECHO timeout=8 >> C:\BOOT.INI
ECHO default=multi(0)disk(0)rdisk(0)partition(2)\WINNT >> C:\BOOT.INI
ECHO [operating systems] >> C:\BOOT.INI
ECHO multi(0)disk(0)rdisk(0)partition(2)\WINNT="Windows 2000 Pro" /fastdetect >> C:\BOOT.INI
ECHO C:\="Windows 98 Second Edition" >> C:\BOOT.INI
:reboot
ECHO Reboot now.[/i]
---------------------------------------
You can replace the last line with a commandline Reboot utility to auto reboot your system after running the batch. Also before runnig this batch you may want to alter it to match your system configuration.
http://download.cnet.com/downloads/0,10150,0-10001-103-0-2-7,00.html?tag=st.dl.10001_103_1.lst.lst&qt=REBOOT&
For some reboot tools.
Thanks, Nitsuj