Interesting post. I looked at building an Atom system, but I ended up deciding against it in the end.
* Why I didn't chose an Atom (Intel Atom D525) or Zacate (AMD E-350):
I'm well aware that a low end Atom or Zacate processor can handle the basic tasks. I'm concerned that I may want to add functionality to this system in the future, and that is where this gets tricky. You can't upgrade an Atom (or Zacate) motherboard. The Atom/E-350 route seems fine for simple tasks, like firewalling or even a NAS, but underpowered for adding any other functionality, including VMs. So Atom is nice, for basic and limited tasks, but you should know that you will hit a performance wall at some point and an upgrade means a new system.
* Why I preferred a Sandy Bridge CPU:
From everything I've read lately, the low power Sandy Bridge CPUs like the Pentium G620T and i3-2100t all seem to have similar power consumption to an Atom or E-350. The added bonus is that I can always upgrade to an i5 (such as i5-2390T) if I feel I need AES-NI to speed up VPNs. In addition, I can even upgrade to a Xeon E3-2130 if I want all of the i5 plus more cache and more threads for an ESXi/Xen/KVM server that can run my PF firewall along with other things. So I feel like I have lots of room for growth. The new Intel S1200KP board has 2x builtin Intel NICs and will support all of the Sandy Bridge CPUs. I've seen really low power consumption rates on this CPU and the D67/H67/H61 chipsets.
In the end, for my home server I chose a Xeon E3-2140 with 16GB RAM. I run Fedora 16 (because it has some the newest Linux KVM features) as a type 2 hypervisor. My VMs include PFSense, SecurityOnion, BackTrack 5, SANS SIFT, CentOS syslog server with Splunk, etc. I do all of this on one system. I no longer have multiple systems creating excess heat and using lots of electricity. When idle, my E3-1240 system uses 40 watts. Yes, that's right, 40 watts. The Sandy Bridge CPU architecture is *very* efficient.
This may not be useful for everyone, but it's worth considering what you want out of an Atom and if your needs will increase in the future.