1 - fenders, not so much to keep the water off you, but everything the water on the road has in it.
2 - Gator shoe covers. I will eventually go the goretex sock/sandal route for warm weather, but use this for cold rain.
3 - Everything in a plastic bag inside my panniers. I use rain covers, too, but don't trust 'em completely.
4 - A rain jacket with lots of vents/pit zips. Breathable is great for doubling as a windbreaker, but zips are a must for rain. I like rain pants that I can unzip half-way up the leg. I'd like rain "chaps" if I could find such a thing to only cover the front of my legs.
5 - Lights!!! Even if you only ride during daylight, you're near invisible in the rain for some reason. Make yourself into a Christmas tree.