I use a Seattle Sports Aquaknot backpack. Room for my company laptop, lunch, and a full set of office clothes, waterproof, comfortable year-round.

When my commute was less urban, I preferred panniers, put the weight on the bike instead of my back, but the backpack offers better stability and control on rough roads, going over curbs, etc. Plus I don't have to take the bag off the bike when racking it up on a bus or train.

Rainy Day Conspicuity - Rear by joshua_putnam, on Flickr

Reflective Flap on Backpack by joshua_putnam, on Flickr