It should be much easier to produce a native 64-bit ArcGIS Server build than a desktop build. When will ArcGIS Server be available in native 64-bit? Likewise, I can't use native 64-but FME Server until the transforms for ESRI formats are supported in native 64-bit. Yes, everything works in 64-bit emulation, but I'm wasting a lot of my expensive hardware!! Not all ESRI formats are supported on native 64-bit FME server - http://www.fmepedia.com/index.php/Can_FME_be_run_on_a_64-bit_machine - particularly usefule would be teh ability to read and write to FGDB in native 64-bit - although that would require Desktop to be native 64-bit.