I am a huge fan of flannel lined jeans. They are kinda pricey (well not pricey compared to but-tight womens hipster jeans) but do the job for most of the winter for me.

The biggest thing you can do bikewise is throw on some full fenders, your feet will almost always get a little slop though, this is where cheapo waterproof hiking boots come in, mine fit in my clips and straps and allow for wool socks, never had cold feet in them (yet).

I always wear a bandana around my neck (be careful if you are in gang territory) and sometimes my neckwarmer (old shirt sleeve with elastic arm band that hugs the nose) comes out of my bag if it is really cold and windy. For gloves, I used to have some nice Outdoor Research mitts (that I used primarily for ice climbing) but lost them (probably drunk) and just use some wool mits when it is "nice" and an old pair of snowmobile gloves when it gets "nasty".

Make sure your ear lobes are covered if it is cold out, you may not be able to feel them before frostbite sets in... trust me, it sucks.

Keep an extra layer in a bag if you plan on riding a long way away from civilization. A breakdown while hot/sweaty will quickly turn to hypothermia if you are not careful. (A dry shirt can be a life-saver).

Winter flats suck, make sure your plastic tire levers don't get brittle and break in the cold.

Don't eat the yellow snow.

A third sock can do wonders for your manhood on long rides (use it like a panty liner, don't "wear" it )