One thing that came up repeatedly at the 3rd Annual Winter Skill Share was the problem of cold toes. I would like to share some of the things I do to keep my tootsies toasty. I have extremely cold toes, so some of this might be overkill for you but like with all things bikey: Your mileage may vary.
Wool wicks away moisture and keeps your feet warm. Sometimes I wear a light merino wool liner sock with thick, wool, knee-high socks. Never EVER wear cotton on your feet.
Boot liners are made out of synthetic fibers or wool and are inserts that go on the bed of your boot. They can be purchased cheaply and last a season or maybe two. They increase the insulation between you and the cold ground. I can usually get another 10 degrees out of my "fall" boots with these.
Air and space in your boots are really important. The cushion of air will insulate your foot and your foot will be able to circulate blood if it has room in your shoe. Your toes will get cold if you foot is squished. Avoid boots that are tight around your foot, wearing too many socks, or using chemical warmers or boot liners if your boot can't accomodate them. If you can't move your toes in your boots, they are too tight.
Tape up the vents on your shoes as the season gets cooler, and eventually you'll want to transition to wearing booties or a non-vented shoe. As winter gets on you'll want to either get a winter cycling shoe ($$$) or a good winter boot ($$) to ride in. A windproof, waterproof, roomy boot that allows movement is a good investment.
I prefer plastic pedals with a big, grippy platform, as opposed to a metal cleat or metal pedal that is going to act as a heat sync on the bottom of your foot as you ride.
Chemical foot warmers are disposable chemical packs that need oxygen to produce heat. I only use these on long rides or when I go to the Art Shantys and I'm going to be standing around on cold ice for a long time. Pro tip: If you are using warmers in your mittens or boots on your commute, put them in an airtight plastic bag when you get to your destination. Squeeze the air out of the bag and seal them in to deactivate them. They will still have some warming power when you reactivate them for your ride home!
Gaiters are a great accessory for closing any gaps in between your pants and your boots. You don't want any chinks in your armor letting a chilly wind in or allowing snow to land in your boots.
I carry enough extra socks so that I can change my socks every time I stop. Dry feet are warm feet, warm feet are happy feet!
When you put pressure on the ball of your foot, you are telling your body to pump blood from your limbs into your core. At red lights, get off of your pedals and shift your weight from foot to foot, stomp, dance, get that blood flowing! Cold blood pooling in your legs will make your toes cold, but it will also chill your whole body once you get off your bike and that chilled blood circulates.
That's the complete guide to hot, hot, footsies. Did I miss anything?