I use one of these in the summer:

http://www.minnehahabags.com/canvas-saddle-bag-medium/

It is as waterproof as you'd usually need and can fit everything I need. I started using it on long distance rides, but I ended up really liking having the weight on the seat rather than swinging off a rack so it found its way onto my commuter as well. I'll usually afix it to my bike with a short length of chain so it can't walk away on me, then use a cloth grocery bag to hold all of my stuff.