You can consider to have, like X8SIA (-F), with three PCI-E slots available pulling from CPU site. You can get more details in the following paths:
http://www.supermicro.com/xeon_3400/Motherboard/X8SIA.cfm?IPMI=N
http://www.supermicro.com/xeon_3400/Motherboard/X8SIA.cfm?IPMI=Y