You have MANY options! However, I have found that chemical toe warmers to be a great addition to whatever you put on your feet when it gets really cold out. These are the brand that I have found to work well:

Grabber Toe Warmers

I only use these on the VERY cold days. They are a bit pricey, but your toes will thank you over, and over again! I run Lake MXZ 300 winter clipless mtb shoes. They are also a bit pricey, but man do they ever work. I use wool, or thick, wicking-type socks underneath. Sporting both the Lakes, and the toe warmers, I can ride all day in the coldest temps, and my feet are always warm.

There are a variety of neoprene booties that also help, but I've only used them over my road shoes to date. They can be found @ you LBS, or any of the on-line shops.

Good luck, and keep those toes warm!!!