========UPDATE==========
OK so I've got the system up and running with just Samba for now, I tried first with FreeNAS to compare performance and they are a lot closer than I thought they would be after reading a few articles on the web criticising FreeNAS's Samba performance. Win 7 drag+drop write was around 60-65MB/s on both and read was about the same. However, according to htop (on Debian) the CPU was nowhere near maxed out (about 15-20% on all cores) so I don't think it's the bottleneck. Iperf with a 2m window size (-s flag on Atom system) reports around 945 Mb/s, again with no cores maxed out but core 1 at about 45%, 2 at 25% and the other 2 at <10%. I'm using ext3 as the share filesystem (on a separate partition to /). However I was a little concerned with temps in the case as the CPU rose to over 70C according to BIOS, IR thermometer was above 50C IIRC and the NM10 was getting pretty toasty too. Neither were close to the max but I think I'll mount a fan in the case somehow to give it some airflow; with the side panel off and an 80mm fan blowing into it the heatsink measures just less than 30C (ambient about 23C). I was considering sticking a VRM heatsink to the NM10 as it runs pretty hot but according to the documentation it's designed to run at up to 113C. Any recommendations for mounting the fan? Also let me know if there's any tests or whatever you'd like to see.
Edit: it seems BIOS CPU temp is inaccurate, it reports about 20 or 70 with no in-between as far as I can tell. The 'remote temp' value seems far more accurate, close to IR thermometer readings.
Edit2: Windows 7 copy speeds (i.e. real-world transfer speeds, not synthetic tests) are reaching between 65 and 100MBps!!
Edit3: Those speeds are without jumbo frames BTW.