Slow Shutdown of Exchange 2003 Server Installed on DC

Method #1: Services kill timeout

Follow these easy steps:
Run Regedit and navigate to
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\WaitToKillServiceTimeout
The default value of WaitToKillServiceTimeout is set to 600000. Change it to 120000.
Exit the registry editor and reboot the server.
Note: Changing the WaitToKillServiceTimeout value may have some undesired effects on other services, use this method at your own risk.

Method #2: Manually stop Exchange related services - my choice

The best choice is to manually shutdown the Exchange related services before trying to shutdown or reboot the server. You can do so manually by going to the Services snap-in in the Administrative Tools menu and stopping the specific Exchange related services, or doing so from the CMD:
net stop MSExchangeES
net stop IMAP4Svc
net stop POP3Svc
net stop RESvc
net stop MSExchangeSRS
net stop MSExchangeMGMT
net stop MSExchangeMTA
net stop MSExchangeIS /Y
net stop MSExchangeSA /Y

http://www.petri.co.il/slow_shutdown_of_exchange_2003_server_installed_on_dc.htm