Viruses aren't generally aimed at the server...
Scob got onto IIS servers through the mail, (MS04-013), Infected and appended malicious script onto its pages. The bad administrator that opens the email gets exploited through outlook, and ends up infecting the footer of every html on the server. (but who checks their email on the webserver anyway?). I don't know if stripping attachments would have held back, scob. I would guess plain texting your emails would stop it (if not thats pretty bad on MS's part).

I would guess that would be one reason for having AV, if you need an automated solution. I guess the future of heuristics is our solution. Take hydan for example... it will make any scanner it's bitch when polymorphism like that is incorporated into malware.