Toes - if you are really serious about riding all winter long and want to keep your clipless pedals invest in some winter riding shoes. I have pair of winter Sidis that I love. I wear them with liner socks and thick wool socks (I kind of have to.... they don't really come small enough for me..), and will add toe warmers when it is very cold.

Fingers - much harder, but smartwool glove liners with a nice thick windproof glove over the top, also adding hand warmers when it is really cold. I still have problems with achy, burning fingers sometimes, but this helps.

It also helps your extremities to keep your core nice and warm - you body won't be trying to steal all of that blood to keep your organs warm, so wear a base layer and windproof layer.