Since I was a kid I've ridden year-round. Living in MI, MN, and the mountains of Colorado, I've had more than my fair share of cold feet through the decades. It wasn't until I started riding and racing in Alaska that I finally got tired of it and decided to do something proactive to prevent permanent damage.
Most folks in AK give up their clipless pedals in the wintertime. I can't pretend to explain such an irrational act using my limited grasp of the English language, so I'll leave it to them to try to confabulate a worthy reason.
I start with a very, very thin liner sock. I've used wool, polypro, silk, and many blends. All work about the same--they move the moisture away from your feet as best they can. All of them stink after just a few uses. As long as you avoid cotton, you're on the right track.
Next I use a vapor barrier liner. Some folks use something like a Subway sandwich bag, which works fine right up until your toes poke a hole through it. The point of the VBL is to keep the sweat produced by your foot from soaking and degrading your insulation. Once your insulation is wet, your feet are cold. Period. I've used the high dollar Black Diamond VBL's on a few trips, and while they're durable and good at keeping the moisture where it's supposed to be, they have many seams that always succeed at rubbing holes and sores into my feet after about day 4. So now I use a thin plastic 'boot' that I got from a bootfitter at the local ski shop.
It's meant to be used when getting custom foam liners fit to your fancy alpine ski boots, but I think I'm giving it a far more dignified life in protecting my insulation from my stinky feet.
Next is the insulation. I use a Sorel felt liner sized ~1/2 size too big for my feet. One of the big 'secrets' to keeping feet warm in winter is giving them room to breathe, which means enough space that you can wiggle your toes easily. What this does is to guarantee that blood is circulating freely. All the insulation in the world is useless if it's clamped too tightly around your foot. The insulation doesn't *produce* any heat--it merely keeps what heat you have available from escaping. So that blood supply is critical because it's the blood that's keeping your feet warm. Nothing else--just the blood.
The Sorel felt liner I use is 12mm thick. If you're a savvy shopper you can find thicknesses from 5mm on up to suit your local temps and needs.
I've got some seriously screwed up ankles from a lifetime of football, basketball, and hockey mishaps, so I need to use a custom orthotic inside of the felt liners. YMMV here. Underneath the orthotic I glued a piece of reflective foam (from a car windshield sunshade) to 'reflect' any heat that makes it's way down back up at me. I doubt it does anything other than satiate my need to know that I at least tried to cover all bases. On top of the orthotic I glued a piece of felt. Very comfy and never cold to the touch.
The outermost layer I use is the Lake MXZ-302 winter cycling shoe. At roughly $270 per pair they are what most folks would consider hideously expensive. I guess it's just a matter of perspective. Having known too many folks with frost damaged feet over the years, I think my toes are worth a few extra dollars. Besides--I wear them 4-5 days a week for three months of every winter, then for roughly three weeks straight when I'm in AK, and I usually get two to three seasons out of a pair. Money well spent, methinks.
The key to this system is sizing the felt liner to your feet, and the outer shoe to fit the felt liner. For reference, I have a size 8.5 foot. I buy a size 9 felt liner, and a size 15 (!) outer shoe. If your feet are bigger than about a size 10, this system will probably not work for you, simply because the outer shoes only go up to size 15 from most manufacturers.
I make a few mods to these to increase traction on ice and to keep overflow from getting in when I have no choice but to dunk my feet at -40 degrees.
This system has evolved slowly over the last decade. If you ride in the lower 48 for less than two hours at a stretch it is overkill for you: For that purpose a pair of the Lake shoes sized 1 to 1.5 sizes too big, with a mid-weight wool sock and a VBL should be plenty. If you ride in the northern US or anywhere in Canada, Alaska, or Northern Europe, my system might be worth further investigation and some fiddling. I've used this setup comfortably down to -65 degrees, and am confident in them to much colder than that. Truthfully, should I ever meet my maker on a winter trip, I think my feet will be the last part of me to freeze. This system really is that good.
If I left out any critical details, please point them out and I'll edit/elaborate later.
Happy winter riding.