For straps, ensure that the bag has a cross-strap (that loops around the other side of your body to the bag), or it will be forever falling off/moving to your front.
For size - I've had a Timbuk2 Medium Messenger, but currently get away with a Timbuk2 Catapult. Certainly this manufacturer has a huge range of colours available, and being able to pick a nice one is a bonus - but it's really the design/comfort (they really think about them being for cyclists) and quality of the product that I was interested in.
Water resistance is an important factor, but it depends on how long your commute is, where in the world you live and whether you're a fair-weather cyclist or not ;-).
It must be comfortable against you. Some bags have more padding than others between it and you. Similarly, if you sit relatively upright or will use it off the bike, a padded strap might be a good idea. If it has a really waterproof, plasticky body, you will sweat buckets against it.
If you intend to take a laptop or tablet, you may want a bag with a dedicated (possibly also padded) section. You may want a zipped up area for various bits and pieces. For bigger bags, you'll definitely want to remove some items from your jersey pockets and place them in the bag. Finally, may want separate sections and stitched pockets for phones, mp3 player, pens, food, wallet, etc. It depends what you take to work and what you leave there. I travel as light as possible - others don't have that choice.