The default System Definition is MacPro3,1 because it works 99.99% of the time for new builders.
However, if you have a Sandy Bridge system and using HD3000 Integrated Graphics with multiple monitors, then a Sys Def of MacMini5,1 works best. MacPro3,1 works fine with Ivy Bridge HD4000 and multiple monitors, though.
If you have power management issues, then the MacPro4,1 or 5,1 might help, but now we talking about experimenting. If you have a 1156 socket system then iMac11,1 might work best for you.
HP ProBooks have found the Sys Def of MacBookPro8,1 works for them with their built-in display.
Finally, the new MacMini6,2 works also on Ivy Bridge systems.
Bottom line -> use the default MacPro3,1 to start out to get your system working, then refine based upon knowledge of others.
Reference:
http://legacy.tonymacx86.com/wiki/index.php/Smbios.plist