Before my sophomore year of college, I was in the market for a laptop bag for a recently acquired 12" powerbook. I ended up getting a backpack with a laptop slot in it, so that I could carry around the laptop without worrying about being a target for theft. I ended up getting a "Mountainsmith Explore" off ebags for $80 at the time (looks like they've gone down a lot in price since then! $48 at the time of writing).
Since then, I've used it around campus, and on several flights (typically 8 per year, often fully loaded with several lbs of stuff I didn't want to include with checked baggage), and after owning it for 4 years now I haven't had a single problem with it. It's gotten rained on, thrown around, and overloaded, and it's still pretty much the same as it was when I got it. I now use it to carry misc things on my commute (~20 mi each way), and the only complaint I have right now is that it keeps my back pretty warm in those conditions. Does a messenger bag help much with this, or is lack of ventilation just something that you get no matter what you use?