He encontrado una lista realmente interesante de exclusiones para los antivirus de los servidores Windows:

Enterprise Configuration Recommendations:

http://support.microsoft.com/kb/822158 

Forefront Configuration:

http://support.microsoft.com/kb/943556

Forefront: 

http://support.microsoft.com/kb/943620

http://technet.microsoft.com/en-us/library/cc707727.aspx

Windows / Active Directory: 

http://support.microsoft.com/kb/822158

http://support.microsoft.com/kb/837932

FRS: 

http://support.microsoft.com/kb/815263

SQL: 
http://support.microsoft.com/kb/309422

IIS:
http://support.microsoft.com/kb/821749 
http://support.microsoft.com/kb/817442

DHCP: 
http://support.microsoft.com/kb/927059

SCOM / MOM:

http://support.microsoft.com/kb/975931

Hyper-V:

http://support.microsoft.com/default.aspx/kb/961804

Exchange:

http://support.microsoft.com/kb/328841

http://support.microsoft.com/kb/823166

http://support.microsoft.com/kb/245822

http://technet.microsoft.com/en-us/library/bb332342(EXCHG.80).aspx

http://technet.microsoft.com/en-us/library/bb332342.aspx

Cluster:

http://support.microsoft.com/kb/250355

SharePoint:

http://support.microsoft.com/kb/320111
http://support.microsoft.com/kb/322941

SMS:

http://support.microsoft.com/kb/327453

ISA:

http://support.microsoft.com/kb/887311

WSUS:

http://support.microsoft.com/kb/900638

SBS:

http://support.microsoft.com/kb/885685