Are you going to use panniers, backpack or do you even need a bag??? Answer this question first and then decide. If you need a bike with panniers, that will narrow your choices down to touring bikes which have all the eyelets for racks and a long chainstay for heel clearance. Trek 520 and surly long haul trucker have long chainstays. I know they are above $1000, but you can find them used for less than $1000 sometimes. If you are just going to be using a backpack, then you can pretty much ride anything, but keep it relatively light and get a bike with fenders since you live in the bay area. Jamis Coda line bikes are a good choice. As are some Kona bikes. Cyclocross bikes make good commuter too especially if you don't need a rack as many don't have eyelets for them.

Come to think about it, a Surly crosscheck would be close to ideal for you. You should be able to find them used for less than a $1000.