Don't know about the memory controllers, and I don't know if that'd be your bottleneck ,... But you might want to consider making the second nic a high speed/good quality Intel chipset card using the high speed PCI express bus/slot that you might normally have put the graphics card in.
Something like this:http://www.cpusolutions.com/store/pc/Intel-Gigabit-CT-Desktop-Adapter-PCI-Express-1-x-RJ-45-10-100-1000Base-T-Internal-p1523.htm?gclid=CJ2pt-nf8bECFUFx4AodxikATA
Personally, as far as even MDs go the middling range of graphics chipsets, even the Intel ones (excepting the PowerVR based ones, if course), are powerful enough to handle 99% of what you'd be throwing at it as a relatively well performing MD. A 3-4 year old Intel GMA 3150 might choke with 1080p playback with the Xine engine (but 90% of content is 720p or lower)... The UI doesn't tax the system much. Beneficial things would be hardware decoder support for media playback, vdpau, etc., more so than triangles per second. Of course, high end graphics cards usually have that too.
I'd also consider pulling the HDs from the MDs,... modest power savings, but more importantly, less heat (MDs are often tucked away). And why waste the drives? Store 'em for later use...