Keeping my toes warm has always been the only thing I struggle with in the winter. I have a couple set ups but neither of them fully do the trick all winter for my commute which takes about 40 minutes each way.

1. Clipless set up - Sidi storm boots, thermal insoles. wool sox, PI Barrier (thick) booties. This is pretty good down to 10F - and i prefer clipless pedals but the off the bike traction of the shoes is not ideal.
2. Platform set up - Garmont Momentum snow hiking boots, wool sox. These are Ok down to about 0F and they are roomy enough for another layer of sox or a chemical warmer when it's below zero.

When it get's below zero I can get still get by with the understanding that my toes will be cold by the end of the ride, It's not a deal breaker, but if I want to be really warm I can throw in a chemical warmer.

I heard a tip the other day, After the ride in, take the chemical warmers and put them in a ziplock bag, the lack of air sort of stops them from working, then pull them out at end of the day, they'll warm up again for the ride home. I haven't tried it yet.