I bike commute to work, so I use a Timbuk2 messenger bag. Its pretty much the greatest thing since sliced bread. They make a laptop messenger, or laptop backpacks. They're super tough, super durable. I just bought a laptop backpack for my upcoming move to Scotland, but my laptop didn't fit the compartment (I have a 15 in. non-mac...they say they'll fit the 15 in. macbook. If I had gotten the bigger backpack, it would have fit, so I'm selling it on ebay.)
www.timbuk2.com
http://www.timbuk2.com/tb2/products/laptop/