These are the folders that should be excluded from Virus Scanning on an SBS 2003 installation. See the Microsoft articles 823166 and 822158 for more information.

c:\inetpub\mailroot\badmail
C:\Program Files\Exchsrvr\***server name here***.log
C:\Program Files\Exchsrvr\conndata
C:\Program Files\Exchsrvr\Mailroot
C:\Program Files\Exchsrvr\mtadata
C:\Program Files\Exchsrvr\srsdata
C:\Program Files\Microsoft Windows Small Business Server\Networking\POP3\Failed Mail
C:\Program Files\Microsoft Windows Small Business Server\Networking\POP3\Incoming Mail
C:\WINDOWS\IIS Temporary Compressed Files
C:\WINDOWS\NTDS
C:\WINDOWS\ntfrs\jet
C:\WINDOWS\SoftwareDistribution\DataStore
C:\WINDOWS\system32\dhcp
C:\WINDOWS\system32\inetsrv
C:\Windows\System32\ntmsdata
C:\WINDOWS\system32\wins
C:\WINDOWS\SYSVOL\staging areas
C:\WINDOWS\SYSVOL\sysvol
C:\windows\temp\Frontpagetempdir

***drive letter and path***\ExchangeData
This last one is assuming that you have correctly taken the decision not to install the Exchange Data on the c:\ drive of your server.

Also of note is that if you are using Trend Micro Client Server Messaging Security for Small and Medium Business version 3.0 and later then the Exchange Data is automatically excluded.