I use a couple different pairs:
The Seirus Storm Socks. These things keep my feet toasty warm. There's a nice thin fleece lining layer in 'em too. * Try the different sizes on before you buy, according to their sizing chart, I should be wearing a Large, but I ended up having to go with XL's b/c i could not get my foot all the way on in the Larges.* You can get these at REI stores. I wear these while skiing and snow shoeing too.
Seirus Stormsocks Socks - Free Shipping at REI.com
The other brand that I go with are these pair of Seal Skinz: 'Submerge.' These socks keep your feet extremely dry, but they are not as warm as the Storm Socks. I usually wear these for those hotter air temp days. *Pro's here are that they do not slip down your leg; they'll stay in place.
SealSkinz Submerge Waterproof Socks - Free Shipping at REI.com
Both of these fit in booties with no problem. They also fit comfortably when wearing them under drysuits.