Overall in winter I'm slower generally. Possible reasons:
More air resistance, both because it is colder and air is more dense, and also because you tend to wear more and bulkier clothes.
Higher winds (even if you get a tailwind one way, you are still less efficient overall).
Supposedly you use more energy in the cold, due to energy used to keep yourself warm or something. Although some studies claim that this isn't an issue for people exercising very hard, only for moderate/light exercise – depends how hard you commute.
Traffic goes slower so you spend more energy stopping and starting while you wait for cars to get out of your way.
More rain – again makes you slower.
More riding in darkness, so you hold back a bit more on the big descents – I know I have one descent I can happily hit >60km/h on in the light, but in the dark I get up to 45-50 (maybe less of an issue in London commutes!).
Joe