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.