The chipset also makes a huge difference. I'm not sure about the more recent versions, but it was almost impossible to find a mini-ITX board with the 945GSE mobile chipset a year ago. Everything had the 945GC chipset. I think the 945GSE had a TDP of ~2W, and the 945GC had a TDP of ~8W (which, I will note, is several times that of the atom! What a waste!) IIRC.
Actually, the 945GSE has a TDP of 6W while the 945GC has a TDP of 22.2W. Meanwhile, the Atom N270 has a TDP of 2.5W while the desktop Atom 230 and 330 have a TDP of 4W and 8W respectively. Hence, for the netbook space, you're looking at 8.5W system TDP while for the desktop variants, you're looking at 26.2W for single-core and 30.2W dual-core.
As others have stated, the chipset matters. Mobile gear is designed to consume less power.
There are low-power Atom chipsets. You'll recognize them by the CPU deisgnation which starts with Z. These consume a good bit less than the usual mobile Atoms systems. I don't know consumers can can buy them separately but I recall Dell sold fanless netbooks based on these. Fit-PC also makes very small desktops featuring that platform.
The codename for the chipset is Poulsbo and the Atom Silverthorne. Chipset is the US15W with TDP of 2.3W and CPU is the Atom Z5xx series with TDP ranging from below 1W to 2.5W (albeit the most common is 2W). It's usually what's inside low power tablets/slates. Hmm, I've actually got a system with this (Viliv X70 EX). I've never measured the power consumption, though.
What are your lowest idle systems with non Atom CPUs?
Lowest idle power, is an Asus UL30A-X5 (Intel GS45 + Core 2 Duo SU7300). Plugged directly into the socket without the battery installed and screen at dimmest, Kill-A-Watt reading is 7W during internet browsing. It has awesome battery life. I believe it even has lower idle power consumption than my brother's Acer netbook. If I remember correctly, that one uses 10W idle (albeit the screen's dimmest setting is brighter than my Asus).